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*  Archaeoglobus - Wikipedia
Another quarter encodes proteins unique to the archaeal domain. One observation about the genome is that there are many gene ... A quarter of the genome encodes preserved proteins whose functions are not yet determined, but are expressed in other archaeons ... However, the possibility that the shared presence of these signature proteins in these archaeal lineages is due to lateral gene ... Comparative genomic studies on archaeal genomes provide evidence that members of the genus Archaeoglobus are the closest ...
  https://en.wikipedia.org/wiki/Archaeoglobus
*  Lateral gene transfer
The degree of conservation preserved in protein sequences in addition to lateral gene transfer between free-living prokaryotes ... archaeal' genes: the gene encoding the large subunit of glutamate synthase (gltB) and the myo-inositol 1P synthase gene (ino1 ... Now that many genomes have been sequenced, scientists can look at the genomes of Drosophila, Arabidopsis, human and more than ... The publicly funded Human Genome Project study indicates that about 0.5% of all human genes were copied into the genome from ...
  http://www.genomenewsnetwork.org/articles/05_01/Lateral_gene_lit.shtml
*  Microbial communities and their predicted metabolic functions in a desiccating acid salt lake | SpringerLink
Dai X, Wang H, Zhang Z et al (2016) Genome sequencing of Sulfolobus sp. A20 from Costa Rica and comparative analyses of the ... De Vries RP, Flitter SJ, Van De Vondervoort PJI et al (2003) Glycerol dehydrogenase, encoded by gldB is essential for ... Edwards KJ, Bond PL, Gihring TM et al (2000) An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. ... Fredrickson JK, Li SW, Gaidamakova EK et al (2008) Protein oxidation: key to bacterial desiccation resistance? ISME J 2:393-403 ...
  https://link.springer.com/article/10.1007/s00792-018-1000-4
*  Frontiers | A calibrated chronology of biochemistry reveals a stem line of descent responsible for planetary biodiversity |...
These timetrees are built from a genomic census of millions of encoded proteins using models of nested accumulation of ... These timetrees are built from a genomic census of millions of encoded proteins using models of nested accumulation of ... Time-calibrated phylogenomic trees of protein domain structure produce powerful chronologies describing the evolution of ... Time-calibrated phylogenomic trees of protein domain structure produce powerful chronologies describing the evolution of ...
  https://www.frontiersin.org/articles/10.3389/fgene.2014.00306/full
*  Archaea Signal Recognition Particle Shows the Way
4. Protein SRP19, Is It Required?. Although protein SRP19 was thought to be absent in certain archaea genomes [3], its genes ( ... The 5e motif, which in eukaryotes binds a 72 kilodalton protein, is preserved in most archaea SRP RNAs despite the lack of an ... H. Maeshima, E. Okuno, T. Aimi, T. Morinaga, and T. Itoh, "An archaeal protein homologous to mammalian SRP54 and bacterial Ffh ... "The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting ...
  https://www.hindawi.com/journals/archaea/2010/485051/
*  Thermoplasma volcanium - Wikipedia
Similar genes encoding HU proteins have been discovered in numerous bacterial genomes, as it is a vital component in many ... 2009). "The stability of the archaeal HU histone-like DNA-binding protein from Thermoplasma volcanium". Extremophiles. 13: 1-10 ... helping to better preserve the environment. Through this method, it may also offer insight into reversing the effects of sulfur ... the genome of Thermoplasma volcanium encodes the histone-like DNA-binding protein HU, found on a segment known as huptvo. ...
  https://en.wikipedia.org/wiki/Thermoplasma_volcanium
*  Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression | Genome...
The ability of such genes to encode functional full-length protein products brings into question their annotation as ... When transcriptional slippage occurs in a coding sequence, translation of the resulting mRNAs yields more than one protein ... This length varies significantly among different bacteria, but in a large proportion of available genomes corresponds to nine ... Comparative sequence analysis of these genomes was used to identify occurrences of 9A and 9T transcriptional slippage-prone ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-3-r25
*  Journal of Cosmology. Origin & Evolution of Life From Other Planets
Indeed, the number of signal transduction and regulatory proteins that are encoded parallel the increasing size of the genome. ... parasitic and symbiotic bacteria and archaeal parasites (e.g., N. equitans) no longer encode or express a variety of protein ... Introns have been preserved often in the same places in the genome, over the course of evolution, be it the genes of Drosophila ... Introns have been preserved often in the same places in the genome, over the course of evolution, be it the genes of Drosophila ...
  http://cosmology.net/Cosmology2.html
*  Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi | BMC Genomics | Full Text
The islands predominantly contained genes putatively involved in biosynthesis of surface layer, genes encoding cell surface ... with cupredoxin domains typically found in archaeal type I copper peripheral membrane proteins. Such proteins, termed ... Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305:567 ... The latter included the gene that encodes the S-layer protein, a gene similar to halomucin that may contribute to capsule ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1794-8
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
... gondii by deleting the gene encoding the KU80 protein1,2. The Δku80 strains behave normally during tachyzoite (acute) and ... The Δku80 strains make functional genomic studies feasible on the single gene as well as on the genome scale1-4. Here, we ... We use methanol as the fixative agent to preserve the spatial distribution of cells. Fixed communities are infiltrated with OCT ... have proven useful for observing spatial organization of bacterial and archaeal communities2,3. A combination of confocal ...
  https://www.jove.com/visualize/abstract/24167557/spatial-structure-facilitates-cooperation-social-dilemma-empirical
*  Publications
"Myelin tetraspan family proteins but no non-tetraspan family proteins are present in the ascidian (Ciona intestinalis) genome. ... "Mouse pigpen encodes a nuclear protein whose expression is developmentally regulated during craniofacial morphogenesis." Dev ... Mehta, M.P., Huber, J.A., and Baross, J.A. (2005). "Incidence of novel and potentially archaeal nitrogenase genes in the deep ... "Alkenone producers inferred from well-preserved 18S rDNA in Greenland lake sediments." Journal of Geophysical Research- ...
  http://www.mbl.edu/jbpc/publicationsparentpage/
*  Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes | Genome Biology |...
... we expect that far more structured RNAs remain to be discovered from bacterial and archaeal organisms. ... By applying a comparative genomics-based approach to genome and metagenome sequences from bacteria and archaea, we identified ... Structured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation ... 1326 defective in cellobiose and xylobiose uptake is mutated in a gene encoding a protein homologous to ATP-binding proteins. ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-3-r31
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
Complex genomes encode at least hundreds of miRNAs, which primarily inhibit the expression of a vast number of target genes ... RISC cleaves the target mRNA thereby reducing the expression of the encoded protein1,2,3. RNAi has become a powerful and widely ... RNA is isolated using a method or reagent that preserves small RNA species, and then labeled with a fluorescence dye. As a ... The interaction of viruses and their prokaryotic hosts shaped the evolution of bacterial and archaeal life. Prokaryotes ...
  https://www.jove.com/visualize/abstract/26147769/assorted-processing-synthetic-trans-acting-sirnas-its-activity
*  Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes
This is true for bacteria belonging to the class Mollicutes that are characterized by reduced genomes and hence considered as ... Most of the 260 known proteins involved in translation have been identified and studied in the bacteria Escherichia coli and ... This analysis allowed us to determine a set of proteins necessary for translation in Mollicutes and define the translation ... Using homology inference approach and expert analyses, we identified the translation apparatus proteins for 39 of these ...
  https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004363
*  Last universal common ancestor - Wikipedia
"The Root of the Universal Tree of Life Inferred from Anciently Duplicated Genes Encoding Components of the Protein-Targeting ... by genetically analyzing 6.1 million protein coding genes from sequenced prokaryotic genomes of various phylogenetic trees, ... Yutin, N.; Makarova K.S.; Mekhedov S.L.; Wolf, Y.I.; Koonin, E.V. (August 2008). "The deep archaeal roots of eukaryotes". ... "Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon". Proceedings of the National Academy of Sciences of the ...
  https://en.wikipedia.org/wiki/Last_universal_common_ancestor
*  Dr GJ Sharples - Durham University
RecBCD and a related host nuclease, SbcCD, are disabled by lambda Gam protein to preserve the ends of the phage genome during ... The mmsA locus of Streptococcus pneumoniae encodes a RecG-like protein involved in DNA repair and in three-strand recombination ... Bolt, E.L., Lloyd, R.G. & Sharples, G.J. (2001). Genetic analysis of an archaeal Holliday junction resolvase in Escherichia ... Bacterial SSB protein blocks access of recombinases. Orf protein therefore serves to load Beta or RecA onto DNA coated with SSB ...
  https://www.dur.ac.uk/wolfson.institute/contacts/staff/?id=37
*  Centre de Biophysique Moléculaire - UPR 4301 - NMR of Biomolecules
Chemical shifts assignments of the archaeal MC1 protein and a strongly bent 15 base pairs DNA duplex in complex Biomolecular ... In most bacteria, HU is a homodimeric protein encoded by a single gene. However, in enterobacteria such as Escherichia coli, ... The genome of all retroviruses consists of two identical copies of an RNA sequence associated in a non-covalent dimer. A region ... The Unusual Resistance of Avian Defensin AvBD7 to Proteolytic Enzymes Preserves Its Antibacterial Activity.. PLoS ONE (2016) 11 ...
  http://cbm.cnrs-orleans.fr/spip.php?article5776
*  Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis...
In addition to the fusions within a single multidomain protein, we identified three groups of HEPN proteins encoded in gene- ... Makarova KS, Wolf YI, Snir S, Koonin EV: Defense islands in bacterial and archaeal genomes and prediction of novel defense ... A subset of the HEPN domains found in these systems preserve the Rx4-6H motif (in large part represented by the DUF86 family in ... and proteins via the DOC toxin. In a similar vein, we found that some PrrC-like proteins are encoded by genomic loci that ...
  https://0-biologydirect-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1745-6150-8-15
*  Conservation and Variability of Synaptonemal Complex Proteins in Phylogenesis of Eukaryotes
... identity with two former proteins [27, 28]. The same is true for the Drosophila protein encoded by gene c(3)G [29, 30] and for ... SC proteins had been isolated and studied experimentally, except D. rerio whose genome was well studied and SC proteins were ... SC protein ASY1 (Arabidopsis thaliana, Euphyllophyta). The archaeal protein RefSeq: YP_003707339.1 (Methanococcus voltae, ... while mitosis preserves the initial chromosome number in both daughter cells. Meiosis is an obligatory component in sexual ...
  https://www.hindawi.com/journals/ijeb/2014/856230/
*  Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in...
Of the two genes that co-occur with the pPIWI-RE gene we found the first to encode a protein with a conserved restriction ... suggesting that the stem eukaryotes could have possibly inherited the ancestral PIWI protein directly from their archaeal ... Gene neighborhoods were extracted and analyzed using a custom PERL script that operates on the Genbank genome or whole genome ... critical residues for guide strand-binding and when preserving the nuclease active site also cleaves the target strand. Prior ...
  https://0-biologydirect-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1745-6150-8-13
*  Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of...
The main phylogenetic patterns for the predicted proteins encoded in six archaeal genomes. Af, Archaeoglobus fulgidus; Mt, ... As far as annotation is concerned, the purpose of primary sequence databases is to faithfully preserve the description attached ... Not unexpectedly, all newly identified A. pernix genes encode small proteins.. Conservation of the core of archaeal COGs shows ... Aeropyrum pernix has been reported to encode 2,694 putative proteins in a 1.67 megabase (Mb) genome [17]. Of these, 633 ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2000-1-5-research0009
*  Evolution of the ribosome at atomic resolution | PNAS
2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known ... Bacterial and archaeal LSU rRNAs are composed entirely of the common core, with only subtle deviations from it. By contrast, ... 2013) Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA 110(14):5294-5300. ... Conformation and base pairing of ancestral helices are preserved upon expansion. Here, taking the conservative assumption that ...
  http://www.pnas.org/content/111/28/10251
*  Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases | BMC Bioinformatics | Full Text
We identified four protein families as new members of the SPOUT superfamily. Three of these families are functionally ... However, no comprehensive comparative analysis of these proteins has been carried out to classify them based on structural and ... We carried out extensive searches of databases of protein structures and sequences to collect all members of previously ... In 2001, when no crystal structures were available for any of these proteins, Anantharaman, Koonin, and Aravind identified ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-73
*  Functional Subunits of Eukaryotic Chaperonin CCT/TRiC in Protein Folding
Ursic D, Ganetzky B. A Drosophila melanogaster gene encodes a protein homologous to the mouse t complex polypeptide 1. Gene. ... Archaeal chaperonins. Frontiers in Bioscience. 2009;14:1304-1324. [PubMed]. 50. Broadley SA, Hartl FU. The role of molecular ... Genome-wide RNA interference screen identifies previously undescribed regulators of polyglutamine aggregation. Proceedings of ... Clinical, pathological, and neurochemical changes in dementia: a subgroup with preserved mental status and numerous neocortical ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC3268035/?lang=en-ca
*  Metazoan Genes Older Than Metazoa? by Brig Klyce
26 Feb 2017: ...the common ancestor ...did encode many of the protein domains of all three super-kingdoms.. 19 Feb 2017: ... Remarkably, many of these [archaeal genomes] contain sequences homologous to genes that play critical roles in the organization ... Preserved in crystal, by Elizabeth McCrocklin, EurekAlert!, 2 Feb 2006. "Scientists at the Weizmann Institute of Science ... 26 Aug 2007: The first analysis of the genome of the sea anemone shows it to be nearly as complex as the human genome.. Richard ...
  https://panspermia.org/oldgenes.htm