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Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases.
Shi R, Shen XX, Rokas A, Eichman BF
(2018) Bioessays 40: e1800133
MeSH Terms: Archaea, Bacteria, Crystallography, X-Ray, DNA, DNA Damage, DNA Glycosylases, DNA Repair, Eukaryota, Protein Conformation
Show Abstract · Added August 26, 2019
DNA glycosylases remove aberrant DNA nucleobases as the first enzymatic step of the base excision repair (BER) pathway. The alkyl-DNA glycosylases AlkC and AlkD adopt a unique structure based on α-helical HEAT repeats. Both enzymes identify and excise their substrates without a base-flipping mechanism used by other glycosylases and nucleic acid processing proteins to access nucleobases that are otherwise stacked inside the double-helix. Consequently, these glycosylases act on a variety of cationic nucleobase modifications, including bulky adducts, not previously associated with BER. The related non-enzymatic HEAT-like repeat (HLR) proteins, AlkD2, and AlkF, have unique nucleic acid binding properties that expand the functions of this relatively new protein superfamily beyond DNA repair. Here, we review the phylogeny, biochemistry, and structures of the HLR proteins, which have helped broaden our understanding of the mechanisms by which DNA glycosylases locate and excise chemically modified DNA nucleobases.
© 2018 WILEY Periodicals, Inc.
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MeSH Terms
Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes.
Wisecaver JH, Alexander WG, King SB, Hittinger CT, Rokas A
(2016) Mol Biol Evol 33: 1979-87
MeSH Terms: Adaptation, Biological, Amino Acid Sequence, Bacteria, Bacterial Proteins, Biological Evolution, Computational Biology, Databases, Nucleic Acid, Dihydropteridine Reductase, Escherichia coli Proteins, Eukaryota, Evolution, Molecular, Fungi, Gene Duplication, Gene Transfer, Horizontal, Hemeproteins, NADH, NADPH Oxidoreductases, Nitric Oxide, Phylogeny
Show Abstract · Added April 6, 2017
Due to their functional independence, proteins that comprise standalone metabolic units, which we name single-protein metabolic modules, may be particularly prone to gene duplication (GD) and horizontal gene transfer (HGT). Flavohemoglobins (flavoHbs) are prime examples of single-protein metabolic modules, detoxifying nitric oxide (NO), a ubiquitous toxin whose antimicrobial properties many life forms exploit, to nitrate, a common source of nitrogen for organisms. FlavoHbs appear widespread in bacteria and have been identified in a handful of microbial eukaryotes, but how the distribution of this ecologically and biomedically important protein family evolved remains unknown. Reconstruction of the evolutionary history of 3,318 flavoHb protein sequences covering the family's known diversity showed evidence of recurrent HGT at multiple evolutionary scales including intrabacterial HGT, as well as HGT from bacteria to eukaryotes. One of the most striking examples of HGT is the acquisition of a flavoHb by the dandruff- and eczema-causing fungus Malassezia from Corynebacterium Actinobacteria, a transfer that growth experiments show is capable of mediating NO resistance in fungi. Other flavoHbs arose via GD; for example, many filamentous fungi possess two flavoHbs that are differentially targeted to the cytosol and mitochondria, likely conferring protection against external and internal sources of NO, respectively. Because single-protein metabolic modules such as flavoHb function independently, readily undergo GD and HGT, and are frequently involved in organismal defense and competition, we suggest that they represent "plug-and-play" proteins for ecological arms races.
© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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18 MeSH Terms
Stephen Elledge and the DNA damage response.
Cortez D, Zhou Z, Sanchez Y
(2015) DNA Repair (Amst) 35: 156-7
MeSH Terms: Awards and Prizes, Biomedical Research, California, DNA Repair, Eukaryota, History, 21st Century, Massachusetts, Texas
Added February 4, 2016
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8 MeSH Terms
Microtubule-regulating kinesins.
Sturgill EG, Ohi R
(2013) Curr Biol 23: R946-8
MeSH Terms: Eukaryota, Humans, Kinesin, Microtubules, Tubulin, Yeasts
Added March 7, 2014
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6 MeSH Terms
Unusual properties of the cytochrome P450 superfamily.
Lamb DC, Waterman MR
(2013) Philos Trans R Soc Lond B Biol Sci 368: 20120434
MeSH Terms: Bacteria, Binding Sites, Biological Evolution, Cytochrome P-450 Enzyme System, Electron Transport, Enzyme Activation, Eukaryota, Heme, Hydroxylation, Models, Molecular, Oxidation-Reduction, Oxygen, Phosphorylation, Protein Binding, Protein Processing, Post-Translational, Protein Structure, Tertiary, Structure-Activity Relationship, Substrate Specificity
Show Abstract · Added February 12, 2015
During the early years of cytochrome P450 research, a picture of conserved properties arose from studies of mammalian forms of these monooxygenases. They included the protohaem prosthetic group, the cysteine residue that coordinates to the haem iron and the reduced CO difference spectrum. Alternatively, the most variable feature of P450s was the enzymatic activities, which led to the conclusion that there are a large number of these enzymes, most of which have yet to be discovered. More recently, studies of these enzymes in other eukaryotes and in prokaryotes have led to the discovery of unexpected P450 properties. Many are variations of the original properties, whereas others are difficult to explain because of their unique nature relative to the rest of the known members of the superfamily. These novel properties expand our appreciation of the broad view of P450 structure and function, and generate curiosity concerning the evolution of P450s. In some cases, structural properties, previously not found in P450s, can lead to enzymatic activities impacting the biological function of organisms containing these enzymes; whereas, in other cases, the biological reason for the variations are not easily understood. Herein, we present particularly interesting examples in detail rather than cataloguing them all.
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18 MeSH Terms
Speciation by symbiosis.
Brucker RM, Bordenstein SR
(2012) Trends Ecol Evol 27: 443-51
MeSH Terms: Bacterial Physiological Phenomena, Biological Evolution, Eukaryota, Genetic Speciation, Models, Biological, Symbiosis
Show Abstract · Added February 8, 2016
In the Origin of Species, Darwin struggled with how continuous changes within a species lead to the emergence of discrete species. Molecular analyses have since identified nuclear genes and organelles that underpin speciation. In this review, we explore the microbiota as a third genetic component that spurs species formation. We first recall Ivan Wallin's original conception from the early 20th century on the role that bacteria play in speciation. We then describe three fundamental observations that justify a prominent role for microbes in eukaryotic speciation, consolidate exemplar studies of microbe-assisted speciation and incorporate the microbiota into classic models of speciation.
Copyright © 2012 Elsevier Ltd. All rights reserved.
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6 MeSH Terms
Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes.
Su Z, Han L, Zhao Z
(2011) Epigenetics 6: 134-40
MeSH Terms: Animals, CpG Islands, Cytosine, DNA Methylation, Embryonic Stem Cells, Epigenomics, Eukaryota, Evolution, Molecular, Fungi, Genome, Humans, Neoplasms, Plants, Sequence Analysis, DNA, Sulfites
Show Abstract · Added March 5, 2014
DNA methylation is one of the most important heritable epigenetic modifications of the genome and is involved in the regulation of many cellular processes. Aberrant DNA methylation has been frequently reported to influence gene expression and subsequently cause various human diseases, including cancer. Recent rapid advances in next-generation sequencing technologies have enabled investigators to profile genome methylation patterns at single-base resolution. Remarkably, more than 20 eukaryotic methylomes have been generated thus far, with a majority published since November 2009. Analysis of this vast amount of data has dramatically enriched our knowledge of biological function, conservation and divergence of DNA methylation in eukaryotes. Even so, many specific functions of DNA methylation and their underlying regulatory systems still remain unknown to us. Here, we briefly introduce current approaches for DNA methylation profiling and then systematically review the features of whole genome DNA methylation patterns in eight animals, six plants and five fungi. Our systematic comparison provides new insights into the conservation and divergence of DNA methylation in eukaryotes and their regulation of gene expression. This work aims to summarize the current state of available methylome data and features informatively.
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15 MeSH Terms
The Prp19 WD40 domain contains a conserved protein interaction region essential for its function.
Vander Kooi CW, Ren L, Xu P, Ohi MD, Gould KL, Chazin WJ
(2010) Structure 18: 584-93
MeSH Terms: Amino Acid Motifs, Crystallography, X-Ray, Eukaryota, Mutagenesis, Protein Structure, Tertiary, Proteins, RNA Splicing, Saccharomyces cerevisiae, Spliceosomes, Ubiquitin-Protein Ligases, X-Rays
Show Abstract · Added March 5, 2014
Prp19 is a member of the WD40 repeat family of E3 ubiquitin ligases and a conserved eukaryotic RNA splicing factor essential for activation and stabilization of the spliceosome. To understand the role of the WD40 repeat domain of Prp19 we have determined its structure using X-ray crystallography. The domain has a distorted seven bladed WD40 architecture with significant asymmetry due to irregular packing of blades one and seven into the core of the WD40 domain. Structure-based mutagenesis identified a highly conserved surface centered around blade five that is required for the physical interaction between Prp19 and Cwc2, another essential splicing factor. This region is found to be required for Prp19 function and yeast viability. Experiments in vitro and in vivo demonstrate that two molecules of Cwc2 bind to the Prp19 tetramer. These coupled structural and functional studies provide a model for the functional architecture of Prp19.
Copyright 2010 Elsevier Ltd. All rights reserved.
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11 MeSH Terms
Protozoan migration in bent microfluidic channels.
Wang W, Shor LM, LeBoeuf EJ, Wikswo JP, Taghon GL, Kosson DS
(2008) Appl Environ Microbiol 74: 1945-9
MeSH Terms: Animals, Ciliophora, Eukaryota, Microfluidic Analytical Techniques
Show Abstract · Added May 29, 2014
Microfluidic devices permit direct observation of microbial behavior in defined microstructured settings. Here, the swimming speed and dispersal of individual marine ciliates in straight and bent microfluidic channels were quantified. The dispersal rate and swimming speed increased with channel width, decreased with protozoan size, and was significantly impacted by the channel turning angle.
1 Communities
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4 MeSH Terms
A novel slow-tight binding serine protease inhibitor from eastern oyster (Crassostrea virginica) plasma inhibits perkinsin, the major extracellular protease of the oyster protozoan parasite Perkinsus marinus.
Xue QG, Waldrop GL, Schey KL, Itoh N, Ogawa M, Cooper RK, Losso JN, La Peyre JF
(2006) Comp Biochem Physiol B Biochem Mol Biol 145: 16-26
MeSH Terms: Amino Acid Sequence, Animals, Base Sequence, Crassostrea, DNA, Complementary, Eukaryota, Kinetics, Molecular Sequence Data, Serine Endopeptidases, Serine Proteinase Inhibitors, Subtilisin
Show Abstract · Added May 27, 2014
A serine protease inhibitor was purified from plasma of the eastern oyster, Crassostrea virginica. The inhibitor is a 7609.6 Da protein consisting of 71 amino acids with 12 cysteine residues that are postulated to form 6 intra-chain disulfide bridges. Sequencing of the cloned cDNA identified an open reading frame encoding a polypeptide of 90 amino acids, with the 19 N-terminal amino acids forming a signal peptide. No sequence similarity with known proteins was found in sequence databases. The protein inhibited the serine proteases subtilisin A, trypsin and perkinsin, the major extracellular protease of the oyster protozoan parasite, Perkinsus marinus, in a slow binding manner. The mechanism of inhibition involves a rapid binding of inhibitor to the enzyme to form a weak enzyme-inhibitor complex followed by a slow isomerization to form a very tight binding enzyme-inhibitor complex. The overall dissociation constants K(i) with subtilisin A, perkinsin and trypsin were 0.29 nM, 13.7 nM and 17.7 nM, respectively. No inhibition of representatives of the other protease classes was detected. This is the first protein inhibitor of proteases identified from a bivalve mollusk and it represents a new protease inhibitor family. Its tight binding to subtilisin and perkinsin suggests it plays a role in the oyster host defense against P. marinus.
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11 MeSH Terms