共查询到20条相似文献,搜索用时 15 毫秒
1.
Background
Escherichia coli guanine-N2 (m2G) methyltransferases (MTases) RsmC and RsmD modify nucleosides G1207 and G966 of 16S rRNA. They possess a common MTase domain in the C-terminus and a variable region in the N-terminus. Their C-terminal domain is related to the YbiN family of hypothetical MTases, but nothing is known about the structure or function of the N-terminal domain. 相似文献2.
Karolina L Tkaczuk Stanislaw Dunin-Horkawicz Elzbieta Purta Janusz M Bujnicki 《BMC bioinformatics》2007,8(1):73
Background
SPOUT methyltransferases (MTases) are a large class of S-adenosyl-L-methionine-dependent enzymes that exhibit an unusual alpha/beta fold with a very deep topological knot. In 2001, when no crystal structures were available for any of these proteins, Anantharaman, Koonin, and Aravind identified homology between SpoU and TrmD MTases and defined the SPOUT superfamily. Since then, multiple crystal structures of knotted MTases have been solved and numerous new homologous sequences appeared in the databases. However, no comprehensive comparative analysis of these proteins has been carried out to classify them based on structural and evolutionary criteria and to guide functional predictions. 相似文献3.
4.
Background
There are several evolutionarily unrelated and structurally dissimilar superfamilies of S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTases). A new superfamily (SPOUT) has been recently characterized on a sequence level and three structures of its members (1gz0, 1ipa, and 1k3r) have been solved. However, none of these structures include the cofactor or the substrate. Due to the strong evolutionary divergence and the paucity of experimental information, no confident predictions of protein-ligand and protein-substrate interactions could be made, which hampered the study of sequence-structure-function relationships in the SPOUT superfamily. 相似文献5.
Janusz M Bujnicki 《BMC evolutionary biology》2002,2(1):3-11
Background
DNA methyltransferases (MTases), unlike MTases acting on other substrates, exhibit sequence permutation. Based on the sequential order of the cofactor-binding subdomain, the catalytic subdomain, and the target recognition domain (TRD), several classes of permutants have been proposed. The majority of known DNA MTases fall into the α, β, and γ classes. There is only one member of the ζ class known and no members of the δ and ε classes have been identified to date. Two mechanisms of permutation have been proposed: one involving gene duplication and in-frame fusion, and the other involving inter- and intragenic shuffling of gene segments. 相似文献6.
7.
Dong Jia Lun Cai Housheng He Geir Skogerbø Tiantian Li Muhammad Nauman Aftab Runsheng Chen 《BMC molecular biology》2007,8(1):86
Background
The 2,2,7-trimethylguanosine (TMG) cap structure is an important functional characteristic of ncRNAs with critical cellular roles, such as some snRNAs. Here we used immunoprecipitation with both K121 and R1131 anti-TMG antibodies to systematically identify the TMG cap structures for all presently characterized ncRNAs in C. elegans. 相似文献8.
Many flaviviruses are significant human pathogens. The plus-strand RNA genome of a flavivirus contains a 5′ terminal cap 1
structure (m7GpppAmG). The flavivirus encodes one methyltransferase (MTase), located at the N-terminal portion of the NS5 RNA-dependent
RNA polymerase (RdRp). Here we review recent advances in our understanding of flaviviral capping machinery and the implications
for drug development. The NS5 MTase catalyzes both guanine N7 and ribose 2′-OH methylations during viral cap formation. Representative
flavivirus MTases, from dengue, yellow fever, and West Nile virus (WNV), sequentially generate GpppA → m7GpppA → m7GpppAm. Despite the existence of two distinct methylation activities, the crystal structures of flavivirus MTases showed a
single binding site for S-adenosyl-L-methionine (SAM), the methyl donor. This finding indicates that the substrate GpppA-RNA
must be repositioned to accept the N7 and 2′-O methyl groups from SAM during the sequential reactions. Further studies demonstrated
that distinct RNA elements are required for the methylations of guanine N7 on the cap and of ribose 2′-OH on the first transcribed
nucleotide. Mutant enzymes with different methylation defects can trans complement one another in vitro, demonstrating that separate molecules of the enzyme can independently catalyze the two cap methylations in vitro. In the context of the infectious virus, defects in both methylations, or a defect in the N7 methylation alone, are lethal
to WNV. However, viruses defective solely in 2′-O methylation are attenuated and can protect mice from later wild-type WNV
challenge. The results demonstrate that the N7 methylation activity is essential for the WNV life cycle and, thus, methyltransferase
represents a novel and promising target for flavivirus therapy. 相似文献
9.
James Murphy Jochen Klumpp Jennifer Mahony Mary O’Connell-Motherway Arjen Nauta Douwe van Sinderen 《BMC genomics》2014,15(1)
Background
So-called 936-type phages are among the most frequently isolated phages in dairy facilities utilising Lactococcus lactis starter cultures. Despite extensive efforts to control phage proliferation and decades of research, these phages continue to negatively impact cheese production in terms of the final product quality and consequently, monetary return.Results
Whole genome sequencing and in silico analysis of three 936-type phage genomes identified several putative (orphan) methyltransferase (MTase)-encoding genes located within the packaging and replication regions of the genome. Utilising SMRT sequencing, methylome analysis was performed on all three phages, allowing the identification of adenine modifications consistent with N-6 methyladenine sequence methylation, which in some cases could be attributed to these phage-encoded MTases. Heterologous gene expression revealed that M.Phi145I/M.Phi93I and M.Phi93DAM, encoded by genes located within the packaging module, provide protection against the restriction enzymes HphI and DpnII, respectively, representing the first functional MTases identified in members of 936-type phages.Conclusions
SMRT sequencing technology enabled the identification of the target motifs of MTases encoded by the genomes of three lytic 936-type phages and these MTases represent the first functional MTases identified in this species of phage. The presence of these MTase-encoding genes on 936-type phage genomes is assumed to represent an adaptive response to circumvent host encoded restriction-modification systems thereby increasing the fitness of the phages in a dynamic dairy environment.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-831) contains supplementary material, which is available to authorized users. 相似文献10.
Alexis Dereeper Stéphane Nicolas Loïc Le Cunff Roberto Bacilieri Agnès Doligez Jean-Pierre Peros Manuel Ruiz Patrice This 《BMC bioinformatics》2011,12(1):134
Background
High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. The rapidly increasing amount of re-sequencing and genotyping data generated by large-scale genetic diversity projects requires the development of integrated bioinformatics tools able to efficiently manage, analyze, and combine these genetic data with genome structure and external data. 相似文献11.
Background
An efficient building block for protein structure prediction can be tripeptides. 8000 different tripeptides from a dataset of 1220 high resolution (≤ 2.0°A) structures from the Protein Data Bank (PDB) have been looked at, to determine which are structurally rigid and non-rigid. This data has been statistically analyzed, discussed and summarized. The entire data can be utilized for the building of protein structures. 相似文献12.
13.
Woon Ching Lee Brian P Anton Susana Wang Primo Baybayan Siddarth Singh Meredith Ashby Eng Guan Chua Chin Yen Tay Fanny Thirriot Mun Fai Loke Khean Lee Goh Barry J Marshall Richard J Roberts Jamuna Vadivelu 《BMC genomics》2015,16(1)
Background
The genome of the human gastric pathogen Helicobacter pylori encodes a large number of DNA methyltransferases (MTases), some of which are shared among many strains, and others of which are unique to a given strain. The MTases have potential roles in the survival of the bacterium. In this study, we sequenced a Malaysian H. pylori clinical strain, designated UM032, by using a combination of PacBio Single Molecule, Real-Time (SMRT) and Illumina MiSeq next generation sequencing platforms, and used the SMRT data to characterize the set of methylated bases (the methylome).Results
The N4-methylcytosine and N6-methyladenine modifications detected at single-base resolution using SMRT technology revealed 17 methylated sequence motifs corresponding to one Type I and 16 Type II restriction-modification (R-M) systems. Previously unassigned methylation motifs were now assigned to their respective MTases-coding genes. Furthermore, one gene that appears to be inactive in the H. pylori UM032 genome during normal growth was characterized by cloning.Conclusion
Consistent with previously-studied H. pylori strains, we show that strain UM032 contains a relatively large number of R-M systems, including some MTase activities with novel specificities. Additional studies are underway to further elucidating the biological significance of the R-M systems in the physiology and pathogenesis of H. pylori.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1585-2) contains supplementary material, which is available to authorized users. 相似文献14.
Tim Van den Bulcke Koenraad Van Leemput Bart Naudts Piet van Remortel Hongwu Ma Alain Verschoren Bart De Moor Kathleen Marchal 《BMC bioinformatics》2006,7(1):43
Background
The development of algorithms to infer the structure of gene regulatory networks based on expression data is an important subject in bioinformatics research. Validation of these algorithms requires benchmark data sets for which the underlying network is known. Since experimental data sets of the appropriate size and design are usually not available, there is a clear need to generate well-characterized synthetic data sets that allow thorough testing of learning algorithms in a fast and reproducible manner. 相似文献15.
Rutger A Vos Jason Caravas Klaas Hartmann Mark A Jensen Chase Miller 《BMC bioinformatics》2011,12(1):63
Background
Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. 相似文献16.
Background
Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. 相似文献17.
Background
Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It is also a fundamental question in Statistics, Data Analysis and Classification, in particular with regard to the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data. 相似文献18.
19.
Background
Population structure analysis is important to genetic association studies and evolutionary investigations. Parametric approaches, e.g. STRUCTURE and L-POP, usually assume Hardy-Weinberg equilibrium (HWE) and linkage equilibrium among loci in sample population individuals. However, the assumptions may not hold and allele frequency estimation may not be accurate in some data sets. The improved version of STRUCTURE (version 2.1) can incorporate linkage information among loci but is still sensitive to high background linkage disequilibrium. Nowadays, large-scale single nucleotide polymorphisms (SNPs) are becoming popular in genetic studies. Therefore, it is imperative to have software that makes full use of these genetic data to generate inference even when model assumptions do not hold or allele frequency estimation suffers from high variation. 相似文献20.