I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition

Advancement in the Breeding, Biotechnological and Genomic Tools towards Development of Durable Genetic Resistance against the Rice Blast Disease

Rice production needs to be sustained in the coming decades, as the changeable climatic conditions are becoming more conducive to disease outbreaks. The majority of rice diseases cause enormous economic damage and yield instability. Among them, rice blast caused by Magnaportheoryzae is a serious fungal disease and is considered one of the major threats to world rice production. This pathogen can infect the above-ground tissues of rice plants at any growth stage and causes complete crop failure under favorable conditions. Therefore, management of blast disease is essentially required to sustain global food production. When looking at the drawback of chemical management strategy, the development of durable, resistant varieties is one of the most sustainable, economic, and environment-friendly approaches to counter the outbreaks of rice blasts. Interestingly, several blast-resistant rice cultivars have been developed with the help of breeding and biotechnological methods. In addition, 146 R genes have been identified, and 37 among them have been molecularly characterized to date. Further, more than 500 loci have been identified for blast resistance which enhances the resources for developing blast resistance through marker-assisted selection (MAS), marker-assisted backcross breeding (MABB), and genome editing tools. Apart from these, a better understanding of rice blast pathogens, the infection process of the pathogen, and the genetics of the immune response of the host plant are very important for the effective management of the blast disease. Further, high throughput phenotyping and disease screening protocols have played significant roles in easy comprehension of the mechanism of disease spread. The present review critically emphasizes the pathogenesis, pathogenomics, screening techniques, traditional and molecular breeding approaches, and transgenic and genome editing tools to develop a broad spectrum and durable resistance against blast disease in rice. The updated and comprehensive information presented in this review would be definitely helpful for the researchers, breeders, and students in the planning and execution of a resistance breeding program in rice against this pathogen.

Agrobacterium: A Genome-Editing Tool-Delivery System

With the rapidly increasing global population, it will be extremely challenging to provide food to the world without increasing food production by at least 70% over the next 30 years. As we reach the limits of expanding arable land, the responsibility of meeting this production goal will rely on increasing yields. Traditional plant breeding practices will not be able to realistically meet these expectations, thrusting plant biotechnology into the limelight to fulfill these needs. Better varieties will need to be developed faster and with the least amount of regulatory hurdles. With the need to add, delete, and substitute genes into existing genomes, the field of genome editing and gene targeting is now rapidly developing with numerous new technologies coming to the forefront. Agrobacterium-mediated crop transformation has been the most utilized method to generate transgenic varieties that are better yielding, have new traits, and are disease and pathogen resistant. Genome-editing technologies rely on the creation of double-strand breaks (DSBs) in the genomic DNA of target species to facilitate gene disruption, addition, or replacement through either non-homologous end joining or homology-dependent repair mechanisms. DSBs can be introduced through the use of zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), or clustered regularly interspersed short palindromic repeats (CRISPR)/Cas nucleases, among others. Agrobacterium strains have been employed to deliver the reagents for genome editing to the specific target cells. Understanding the biology of transformation from the perspective not only of Agrobacterium, but also of the host, from processing of T-DNA to its integration in the host genome, has resulted in a wealth of information that has been used to engineer Agrobacterium strains having increased virulence. As more technologies are being developed, that will help overcome issues of Agrobacterium host range and random integration of DNA, combined with highly sequence-specific nucleases, a robust crop genome-editing toolkit finally seems attainable.

Genomics Approaches For Improving Salinity Stress Tolerance in Crop Plants

Salinity is one of the major factors which reduces crop production worldwide. Plant responses to salinity are highly complex and involve a plethora of genes. Due to its multigenicity, it has been difficult to attain a complete understanding of how plants respond to salinity. Genomics has progressed tremendously over the past decade and has played a crucial role towards providing necessary knowledge for crop improvement. Through genomics, we have been able to identify and characterize the genes involved in salinity stress response, map out signaling pathways and ultimately utilize this information for improving the salinity tolerance of existing crops. The use of new tools, such as gene pyramiding, in genetic engineering and marker assisted breeding has tremendously enhanced our ability to generate stress tolerant crops. Genome editing technologies such as Zinc finger nucleases, TALENs and CRISPR/Cas9 also provide newer and faster avenues for plant biologists to generate precisely engineered crops.

Molecular scissors and their application in genetically modified farm animals

Molecular scissors (MS), incl. Zinc Finger Nucleases (ZFN), Transcription-activator like endoncleases (TALENS) and meganucleases possess long recognition sites and are thus capable of cutting DNA in a very specific manner. These molecular scissors mediate targeted genetic alterations by enhancing the DNA mutation rate via induction of double-strand breaks at a predetermined genomic site. Compared to conventional homologous recombination based gene targeting, MS can increase the targeting rate 10,000-fold, and gene disruption via mutagenic DNA repair is stimulated at a similar frequency. The successful application of different MS has been shown in different organisms, including insects, amphibians, plants, nematodes, and mammals, including humans. Recently, another novel class of molecular scissors was described that uses RNAs to target a specific genomic site. The CRISPR/Cas9 system is capable of targeting even multiple genomic sites in one shot and thus could be superior to ZFNs or TALEN, especially by its easy design. MS can be successfully employed for improving the understanding of complex physiological systems, producing transgenic animals, incl. creating large animal models for human diseases, creating specific cell lines, and plants, and even for treating human genetic diseases. This review provides an update on molecular scissors, their underlying mechanism and focuses on new opportunities for generating genetically modified farm animals.

AAV-mediated gene editing via double-strand break repair

Traditionally, the ability to edit the mammalian genome was inhibited by the inherent low efficiency of homologous recombination (HR; approximately <1 in a million events) and the inability to deliver DNA efficiently to dividing and non-dividing cells/tissue. Despite these limitations, creative selections designed over 20 years ago, clearly demonstrated the powerful implications of gene knock-in and knockout technology for the genetic engineering of mice (Doetschman et al. Nat 330(6148): 576-578, 1987; Thomas and Capecchi. Cell 51(3): 503-512, 1987). The development and application of recombinant vectors based on adeno-associated virus (rAAV) have helped to overcome both of the initial limitations regarding DNA delivery and the frequency of HR. Considering DNA delivery, rAAV infects non-dividing and dividing cultured cells as well as most tissues in mouse and larger animal models (including humans). At the DNA editing level, rAAV genomes have been reported to increase the frequency of HR several orders of magnitude by serving as the repair substrate (Russell and Hirata. Nat Genet 18(4): 325-330, 1998). However, reports on the ability of rAAV genomes to stimulate HR, compared to plasmid DNA and oligonucleotides, are variable, and many labs have found it necessary to augment the frequency of rAAV-induced HR using site-specific endonucleases (Ellis et al. Gene Ther, 2012; Hirsch et al. Gene Ther 17(9): 1175-1180, 2010; Porteus et al. Mol Cell Biol 23(10): 3558-3565, 2003; Radecke et al. Mol Ther 14(6): 798-808, 2006). In this protocol, we describe a method to perform rAAV-mediated double-strand break (DSB) repair for precise genetic engineering in human cells.

Homing endonucleases: from genetic anomalies to programmable genomic clippers

Homing endonucleases are strong drivers of genetic exchange and horizontal transfer of both their own genes and their local genetic environment. The mechanisms that govern the function and evolution of these genetic oddities have been well documented over the past few decades at the genetic, biochemical, and structural levels. This wealth of information has led to the manipulation and reprogramming of the endonucleases and to their exploitation in genome editing for use as therapeutic agents, for insect vector control and in agriculture. In this chapter we summarize the molecular properties of homing endonucleases and discuss their strengths and weaknesses in genome editing as compared to other site-specific nucleases such as zinc finger endonucleases, TALEN, and CRISPR-derived endonucleases.

Group I introns in Staphylococcus bacteriophages

The abundance of group I introns, intragenic RNA sequences capable of self-splicing, in Gram-positive bacteriophage genomes, is illustrated by various new group I introns recently described in Staphylococcus phage genomes. These introns were found to interrupt DNA metabolism genes as well as late genes. These group I introns often code for homing endonucleases, which promote lateral transfer of group I introns, thereby enabling spread through a population. Homing endonucleases encoded by group I introns in Staphylococcus phage genomes were predicted to belong to the GIY-YIG, LAGLIDADG, HNH or EDxHD family of endonucleases. The group I intron distribution in Staphylococcus phage genomes exemplifies the homology between these introns as well as the encoded endonucleases. Despite several suggested functions, the role of group I introns in bacteriophages remains unclear or might be nonexistent. However, transcriptome analysis might provide additional information to elucidate the possible purpose of group I introns in phage genomes.

qDTY12.1: a locus with a consistent effect on grain yield under drought in rice

Background

Selection for grain yield under drought is an efficient criterion for improving the drought tolerance of rice. Recently, some drought-tolerant rice varieties have been developed using this selection criterion and successfully released for cultivation in drought-prone target environments. The process can be made more efficient and rapid through marker-assisted breeding, a well-known fast-track approach in crop improvement. QTLs have been identified for grain yield under drought with large effects against drought-susceptible varieties. Most of the identified QTLs show large QTL × environment or QTL × genetic background interactions. The development of mapping populations in the background of popular high-yielding varieties, screening across environments, including the target environments, and the identification of QTLs with a consistent effect across environments can be a suitable alternative marker-assisted breeding strategy. An IR74371-46-1-1 × Sabitri backcross inbred line population was screened for reproductive-stage drought stress at the International Rice Research Institute, Philippines, and Regional Agricultural Research Station, Nepalgunj, Nepal, in the dry and wet seasons of 2011, respectively. A bulk segregant analysis approach was used to identify markers associated with high grain yield under drought.

Results

A QTL, qDTY_12.1, significantly associated with grain yield under reproductive-stage drought stress was identified on chromosome 12 with a consistent effect in two environments: IRRI, Philippines, and RARS, Nepalgunj, Nepal. This QTL explained phenotypic variance of 23.8% and contributed an additive effect of 45.3% for grain yield under drought. The positive QTL allele for qDTY_12.1 was contributed by tolerant parent IR74371-46-1-1.

Conclusions

In this study, qDTY_12.1 showed a consistent effect across environments for high grain yield under lowland reproductive-stage drought stress in the background of popular high-yielding but drought-susceptible recipient variety Sabitri. qDTY_12.1 was also reported previously [Crop Sci 47:507–516, 2007] to increase grain yield under upland reproductive-stage drought stress situations. qDTY_12.1 is the only QTL reported so far in rice to have shown a large effect against multiple recipient genetic backgrounds as well as under highly diverse upland and lowland rice ecosystems. qDTY_12.1 can be successfully introgressed to improve grain yield under drought of popular high-yielding but drought-susceptible lowland as well as upland adapted varieties following marker-assisted breeding.

Homing endonucleases: DNA scissors on a mission

Buried within the genomes of many microorganisms are genetic elements that encode rare-cutting homing endonucleases that assist in the mobility of the elements that encode them, such as the self-splicing group I and II introns and in some cases inteins. There are several different families of homing endonucleases and their ability to initiate and target specific sequences for lateral transfers makes them attractive reagents for gene targeting. Homing endonucleases have been applied in promoting DNA modification or genome editing such as gene repair or "gene knockouts". This review examines the categories of homing endonucleases that have been described so far and their possible applications to biotechnology. Strategies to engineer homing endonucleases to alter target site specificities will also be addressed. Alternatives to homing endonucleases such as zinc finger nucleases, transcription activator-like effector nucleases, triplex forming oligonucleotide nucleases, and targetrons are also briefly discussed.

Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities

BACKGROUND

We previously defined a family of restriction endonucleases (REases) from Thermus sp., which share common biochemical and biophysical features, such as the fusion of both the nuclease and methyltransferase (MTase) activities in a single polypeptide, cleavage at a distance from the recognition site, large molecular size, modulation of activity by S-adenosylmethionine (SAM), and incomplete cleavage of the substrate DNA. Members include related thermophilic REases with five distinct specificities: TspGWI, TaqII, Tth111II/TthHB27I, TspDTI and TsoI.

RESULTS

TspDTI, TsoI and isoschizomers Tth111II/TthHB27I recognize different, but related sequences: 5'-ATGAA-3', 5'-TARCCA-3' and 5'-CAARCA-3' respectively. Their amino acid sequences are similar, which is unusual among REases of different specificity. To gain insight into this group of REases, TspDTI, the prototype member of the Thermus sp. enzyme family, was cloned and characterized using a recently developed method for partially cleaving REases.

CONCLUSIONS

TspDTI, TsoI and isoschizomers Tth111II/TthHB27I are closely related bifunctional enzymes. They comprise a tandem arrangement of Type I-like domains, like other Type IIC enzymes (those with a fusion of a REase and MTase domains), e.g. TspGWI, TaqII and MmeI, but their sequences are only remotely similar to these previously characterized enzymes. The characterization of TspDTI, a prototype member of this group, extends our understanding of sequence-function relationships among multifunctional restriction-modification enzymes.

Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms

Homing endonucleases (HEs) are highly specific DNA-cleaving enzymes that are encoded by invasive DNA elements (usually mobile introns or inteins) within the genomes of phage, bacteria, archea, protista and eukaryotic organelles. Six unique structural HE families, that collectively span four distinct nuclease catalytic motifs, have been characterized to date. Members of each family display structural homology and functional relationships to a wide variety of proteins from various organisms. The biological functions of those proteins are highly disparate and include non-specific DNA-degradation enzymes, restriction endonucleases, DNA-repair enzymes, resolvases, intron splicing factors and transcription factors. These relationships suggest that modern day HEs share common ancestors with proteins involved in genome fidelity, maintenance and gene expression. This review summarizes the results of structural studies of HEs and corresponding proteins from host organisms that have illustrated the manner in which these factors are related.

Towards artificial metallonucleases for gene therapy: recent advances and new perspectives

The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.

Meganucleases and other tools for targeted genome engineering: perspectives and challenges for gene therapy

The importance of safer approaches for gene therapy has been underscored by a series of severe adverse events (SAEs) observed in patients involved in clinical trials for Severe Combined Immune Deficiency Disease (SCID) and Chromic Granulomatous Disease (CGD). While a new generation of viral vectors is in the process of replacing the classical gamma-retrovirus-based approach, a number of strategies have emerged based on non-viral vectorization and/or targeted insertion aimed at achieving safer gene transfer. Currently, these methods display lower efficacies than viral transduction although many of them can yield more than 1% of engineered cells in vitro. Nuclease-based approaches, wherein an endonuclease is used to trigger site-specific genome editing, can significantly increase the percentage of targeted cells. These methods therefore provide a real alternative to classical gene transfer as well as gene editing. However, the first endonuclease to be in clinic today is not used for gene transfer, but to inactivate a gene (CCR5) required for HIV infection. Here, we review these alternative approaches, with a special emphasis on meganucleases, a family of naturally occurring rare-cutting endonucleases, and speculate on their current and future potential.

The I-CreI meganuclease and its engineered derivatives: applications from cell modification to gene therapy

Meganucleases (MNs) are highly specific enzymes that can induce homologous recombination in different types of cells, including mammalian cells. Consequently, these enzymes are used as scaffolds for the development of custom gene-targeting tools for gene therapy or cell-line development. Over the past 15 years, the high resolution X-ray structures of several MNs from the LAGLIDADG family have improved our understanding of their protein-DNA interaction and mechanism of DNA cleavage. By developing and utilizing high-throughput screening methods to test a large number of variant-target combinations, we have been able to re-engineer scores of I-CreI derivatives into custom enzymes that target a specific DNA sequence of interest. Such customized MNs, along with wild-type ones, have allowed for exploring a large range of biotechnological applications, including protein-expression cell-line development, genetically modified plants and animals and therapeutic applications such as targeted gene therapy as well as a novel class of antivirals.

Homing endonucleases: from basics to therapeutic applications

Homing endonucleases (HE) are double-stranded DNAses that target large recognition sites (12-40 bp). HE-encoding sequences are usually embedded in either introns or inteins. Their recognition sites are extremely rare, with none or only a few of these sites present in a mammalian-sized genome. However, these enzymes, unlike standard restriction endonucleases, tolerate some sequence degeneracy within their recognition sequence. Several members of this enzyme family have been used as templates to engineer tools to cleave DNA sequences that differ from their original wild-type targets. These custom HEs can be used to stimulate double-strand break homologous recombination in cells, to induce the repair of defective genes with very low toxicity levels. The use of tailored HEs opens up new possibilities for gene therapy in patients with monogenic diseases that can be treated ex vivo. This review provides an overview of recent advances in this field.

Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family

Background

Restriction-modification systems are a diverse class of enzymes. They are classified into four major types: I, II, III and IV. We have previously proposed the existence of a Thermus sp. enzyme family, which belongs to type II restriction endonucleases (REases), however, it features also some characteristics of types I and III. Members include related thermophilic endonucleases: TspGWI, TaqII, TspDTI, and Tth111II.

Results

Here we describe cloning, mutagenesis and analysis of the prototype TspGWI enzyme that recognises the 5'-ACGGA-3' site and cleaves 11/9 nt downstream. We cloned, expressed, and mutagenised the tspgwi gene and investigated the properties of its product, the bifunctional TspGWI restriction/modification enzyme. Since TspGWI does not cleave DNA completely, a cloning method was devised, based on amino acid sequencing of internal proteolytic fragments. The deduced amino acid sequence of the enzyme shares significant sequence similarity with another representative of the Thermus sp. family – TaqII. Interestingly, these enzymes recognise similar, yet different sequences in the DNA. Both enzymes cleave DNA at the same distance, but differ in their ability to cleave single sites and in the requirement of S-adenosylmethionine as an allosteric activator for cleavage. Both the restriction endonuclease (REase) and methyltransferase (MTase) activities of wild type (wt) TspGWI (either recombinant or isolated from Thermus sp.) are dependent on the presence of divalent cations.

Conclusion

TspGWI is a bifunctional protein comprising a tandem arrangement of Type I-like domains; particularly noticeable is the central HsdM-like module comprising a helical domain and a highly conserved S-adenosylmethionine-binding/catalytic MTase domain, containing DPAVGTG and NPPY motifs. TspGWI also possesses an N-terminal PD-(D/E)XK nuclease domain related to the corresponding domains in HsdR subunits, but lacks the ATP-dependent translocase module of the HsdR subunit and the additional domains that are involved in subunit-subunit interactions in Type I systems. The MTase and REase activities of TspGWI are autonomous and can be uncoupled. Structurally and functionally, the TspGWI protomer appears to be a streamlined 'half' of a Type I enzyme.

A likely pathway for formation of mobile group I introns

Mobile group I introns are RNA splicing elements that have been invaded by endonuclease genes. These endonucleases facilitate intron mobility by a unidirectional, duplicative gene-conversion process known as homing [1]. Survival of the invading endonuclease depends upon its ability to promote intron mobility. Therefore, the endonuclease must either quickly change its cleavage specificity to match the site of intron insertion, or it must already be preadapted to cleave this sequence. Here we show that the group I intron in the DNA polymerase gene of T7-like bacteriophage PhiI is mobile, dependent upon its intronic HNH homing endonuclease gene, I-TslI. We also show that gene 5.3 of phage T3, located adjacent to its intronless DNA polymerase gene, is a homologous homing endonuclease gene whose protein product initiates efficient spread of gene 5.3 into empty sites in related phages. Both of these endonucleases cleave intronless DNA polymerase genes at identical positions. This shared feature between an intronic and free-standing endonuclease is unprecedented. Based on this evidence, we propose that introns and their homing endonucleases evolve separately to target the same highly conserved sequences, uniting afterwards to create a composite mobile element.

Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I

The restriction endonuclease fold [a three-layer alpha-beta sandwich containing variations of the PD-(D/E)XK nuclease motif] has been greatly diversified during evolution, facilitating its use for many biological functions. Here we characterize DNA binding and cleavage by the PD-(D/E)XK homing endonuclease I-Ssp6803I. Unlike most restriction endonucleases harboring the same core fold, the specificity profile of this enzyme extends over a long (17 bp) target site. The DNA binding and cleavage specificity profiles of this enzyme were independently determined and found to be highly correlated. However, the DNA target sequence contains several positions where binding and cleavage activities are not tightly coupled: individual DNA base-pair substitutions at those positions that significantly decrease cleavage activity have minor effects on binding affinity. These changes in the DNA target sequence appear to correspond to substitutions that uniquely increase the free energy change between the ground state and the transition state, rather than simply decreasing the overall DNA binding affinity. The specificity of the enzyme reflects constraints on its host gene and limitations imposed by the enzyme's quaternary structure and illustrate the highly diverse repertoire of DNA recognition specificities that can be adopted by the related folds surrounding the PD-(D/E)XK nuclease motif.

MetaMQAP: a meta-server for the quality assessment of protein models

Background

Computational models of protein structure are usually inaccurate and exhibit significant deviations from the true structure. The utility of models depends on the degree of these deviations. A number of predictive methods have been developed to discriminate between the globally incorrect and approximately correct models. However, only a few methods predict correctness of different parts of computational models. Several Model Quality Assessment Programs (MQAPs) have been developed to detect local inaccuracies in unrefined crystallographic models, but it is not known if they are useful for computational models, which usually exhibit different and much more severe errors.

Results

The ability to identify local errors in models was tested for eight MQAPs: VERIFY3D, PROSA, BALA, ANOLEA, PROVE, TUNE, REFINER, PROQRES on 8251 models from the CASP-5 and CASP-6 experiments, by calculating the Spearman's rank correlation coefficients between per-residue scores of these methods and local deviations between C-alpha atoms in the models vs. experimental structures. As a reference, we calculated the value of correlation between the local deviations and trivial features that can be calculated for each residue directly from the models, i.e. solvent accessibility, depth in the structure, and the number of local and non-local neighbours. We found that absolute correlations of scores returned by the MQAPs and local deviations were poor for all methods. In addition, scores of PROQRES and several other MQAPs strongly correlate with 'trivial' features. Therefore, we developed MetaMQAP, a meta-predictor based on a multivariate regression model, which uses scores of the above-mentioned methods, but in which trivial parameters are controlled. MetaMQAP predicts the absolute deviation (in Ångströms) of individual C-alpha atoms between the model and the unknown true structure as well as global deviations (expressed as root mean square deviation and GDT_TS scores). Local model accuracy predicted by MetaMQAP shows an impressive correlation coefficient of 0.7 with true deviations from native structures, a significant improvement over all constituent primary MQAP scores. The global MetaMQAP score is correlated with model GDT_TS on the level of 0.89.

Conclusion

Finally, we compared our method with the MQAPs that scored best in the 7th edition of CASP, using CASP7 server models (not included in the MetaMQAP training set) as the test data. In our benchmark, MetaMQAP is outperformed only by PCONS6 and method QA_556 – methods that require comparison of multiple alternative models and score each of them depending on its similarity to other models. MetaMQAP is however the best among methods capable of evaluating just single models.

We implemented the MetaMQAP as a web server available for free use by all academic users at the URL

Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses

For a very long time, Type II restriction enzymes (REases) have been a paradigm of ORFans: proteins with no detectable similarity to each other and to any other protein in the database, despite common cellular and biochemical function. Crystallographic analyses published until January 2008 provided high-resolution structures for only 28 of 1637 Type II REase sequences available in the Restriction Enzyme database (REBASE). Among these structures, all but two possess catalytic domains with the common PD-(D/E)XK nuclease fold. Two structures are unrelated to the others: R.BfiI exhibits the phospholipase D (PLD) fold, while R.PabI has a new fold termed 'half-pipe'. Thus far, bioinformatic studies supported by site-directed mutagenesis have extended the number of tentatively assigned REase folds to five (now including also GIY-YIG and HNH folds identified earlier in homing endonucleases) and provided structural predictions for dozens of REase sequences without experimentally solved structures. Here, we present a comprehensive study of all Type II REase sequences available in REBASE together with their homologs detectable in the nonredundant and environmental samples databases at the NCBI. We present the summary and critical evaluation of structural assignments and predictions reported earlier, new classification of all REase sequences into families, domain architecture analysis and new predictions of three-dimensional folds. Among 289 experimentally characterized (not putative) Type II REases, whose apparently full-length sequences are available in REBASE, we assign 199 (69%) to contain the PD-(D/E)XK domain. The HNH domain is the second most common, with 24 (8%) members. When putative REases are taken into account, the fraction of PD-(D/E)XK and HNH folds changes to 48% and 30%, respectively. Fifty-six characterized (and 521 predicted) REases remain unassigned to any of the five REase folds identified so far, and may exhibit new architectures. These enzymes are proposed as the most interesting targets for structure determination by high-resolution experimental methods. Our analysis provides the first comprehensive map of sequence-structure relationships among Type II REases and will help to focus the efforts of structural and functional genomics of this large and biotechnologically important class of enzymes.

HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling

Type I restriction-modification (RM) systems are large, multifunctional enzymes composed of three different subunits. HsdS and HsdM form a complex in which HsdS recognizes the target DNA sequence, and HsdM carries out methylation of adenosine residues. The HsdR subunit, when associated with the HsdS-HsdM complex, translocates DNA in an ATP-dependent process and cleaves unmethylated DNA at a distance of several thousand base-pairs from the recognition site. The molecular mechanism by which these enzymes translocate the DNA is not fully understood, in part because of the absence of crystal structures. To date, crystal structures have been determined for the individual HsdS and HsdM subunits and models have been built for the HsdM-HsdS complex with the DNA. However, no structure is available for the HsdR subunit. In this work, the gene coding for the HsdR subunit of EcoR124I was re-sequenced, which showed that there was an error in the published sequence. This changed the position of the stop codon and altered the last 17 amino acid residues of the protein sequence. An improved purification procedure was developed to enable HsdR to be purified efficiently for biophysical and structural analysis. Analytical ultracentrifugation shows that HsdR is monomeric in solution, and the frictional ratio of 1.21 indicates that the subunit is globular and fairly compact. Small angle neutron-scattering of the HsdR subunit indicates a radius of gyration of 3.4 nm and a maximum dimension of 10 nm. We constructed a model of the HsdR using protein fold-recognition and homology modelling to model individual domains, and small-angle neutron scattering data as restraints to combine them into a single molecule. The model reveals an ellipsoidal shape of the enzymatic core comprising the N-terminal and central domains, and suggests conformational heterogeneity of the C-terminal region implicated in binding of HsdR to the HsdS-HsdM complex.

Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns

BACKGROUND

Group I introns are one of the four major classes of introns as defined by their distinct splicing mechanisms. Because they catalyze their own removal from precursor transcripts, group I introns are referred to as autocatalytic introns. Group I introns are common in fungal and protist nuclear ribosomal RNA genes and in organellar genomes. In contrast, they are rare in all other organisms and genomes, including bacteria.

RESULTS

Here we report five group I introns, each containing a LAGLIDADG homing endonuclease gene (HEG), in large subunit (LSU) rRNA genes of cyanobacteria. Three of the introns are located in the LSU gene of Synechococcus sp. C9, and the other two are in the LSU gene of Synechococcus lividus strain C1. Phylogenetic analyses show that these introns and their HEGs are closely related to introns and HEGs located at homologous insertion sites in organellar and bacterial rDNA genes. We also present a compilation of group I introns with homing endonuclease genes in bacteria.

CONCLUSION

We have discovered multiple HEG-containing group I introns in a single bacterial gene. To our knowledge, these are the first cases of multiple group I introns in the same bacterial gene (multiple group I introns have been reported in at least one phage gene and one prophage gene). The HEGs each contain one copy of the LAGLIDADG motif and presumably function as homodimers. Phylogenetic analysis, in conjunction with their patchy taxonomic distribution, suggests that these intron-HEG elements have been transferred horizontally among organelles and bacteria. However, the mode of transfer and the nature of the biological connections among the intron-containing organisms are unknown.

The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif

The homing endonuclease I-Ssp6803I causes the insertion of a group I intron into a bacterial tRNA gene-the only example of an invasive mobile intron within a bacterial genome. Using a computational fold prediction, mutagenic screen and crystal structure determination, we demonstrate that this protein is a tetrameric PD-(D/E)-XK endonuclease - a fold normally used to protect a bacterial genome from invading DNA through the action of restriction endonucleases. I-Ssp6803I uses its tetrameric assembly to promote recognition of a single long target site, whereas restriction endonuclease tetramers facilitate cooperative binding and cleavage of two short sites. The limited use of the PD-(D/E)-XK nucleases by mobile introns stands in contrast to their frequent use of LAGLIDADG and HNH endonucleases - which in turn, are rarely incorporated into restriction/modification systems.