*  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
*  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
*  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
*  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/
*  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
*  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
*  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
*  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
*  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
*  ERCC1 - Wikipedia
DNA excision repair protein ERCC-1 is a protein that in humans is encoded by the ERCC1 gene. Together with ERCC4, ERCC1 forms ... Ercc1 mutant mice dietary restriction while delaying aging also attenuates accumulation of genome-wide DNA damage and preserves ... Sgouros J, Gaillard PH, Wood RD (Mar 1999). "A relationship between a DNA-repair/recombination nuclease family and archaeal ... During NER, the ERCC1 protein interacts with the XPA protein to coordinate DNA and protein binding. Mammalian cells with mutant ...
  https://en.wikipedia.org/wiki/ERCC1
*  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
*  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
*  Publications | Microbial Ecology, University of Vienna
The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92 RNA genes. One striking feature of this ... The candidate archaeal phylum 'Aigarchaeota' contains microorganisms from terrestrial and subsurface geothermal ecosystems. The ... Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic ... We found an unusually large number of genes encoding proteins with eukaryotic-like domains such as ankyrins, leucine-rich ...
  http://dome.csb.univie.ac.at/publications?id=939
*  The Evolution of Complex Life on Earth
Bacterial and archaeal encoded enzymes catalyze all the major processes involved in global biogeochemical cycling, playing key ... genome expansion, life on Earth, membranes, mitochondria, prokaryotic, protein folds, ribosomes, transition to complex life on ... When sectioned very thinly, fossil stromatolites may be found to contain exquisitely preserved fossil cyanobacteria and algae. ... Eukaryotes invented five times as many protein folds as eubacteria, and ten times as many as archaea. Even median protein ...
  https://sciencepolicyivh.wordpress.com/2015/02/22/the-evolution-of-complex-life-on-earth/
*  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
*  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
*  Archaea - Wikipedia
... of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no ... 19 October 2015). "Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon" (PDF). Proceedings of the National ... The tiny 490,885 base-pair genome of Nanoarchaeum equitans is one-tenth of this size and the smallest archaeal genome known; it ... of the ARMAN group of archaea Genomics Browse any completed archaeal genome at UCSC Comparative Analysis of Archaeal Genomes ( ...
  https://en.wikipedia.org/wiki/Archaea
*  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
*  Almostbest
A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure. ... Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. ... Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. ... Relating whole-genome expression data with protein-protein interactions.. R Jansen, D Greenbaum, M Gerstein (2002). Genome Res ...
  http://papers.gersteinlab.org/subject/almostbest/
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
Protein, Protein Binding, Computational Biology, Drug Design, optimization (mathematics), Amino Acids, Peptides, and Proteins, ... Genetically encoded Ca2+ indicators that are targeted to different cellular compartments have provided a platform for live cell ... We use methanol as the fixative agent to preserve the spatial distribution of cells. Fixed communities are infiltrated with OCT ... Combining Magnetic Sorting of Mother Cells and Fluctuation Tests to Analyze Genome Instability During Mitotic Cell Aging in ...
  https://www.jove.com/visualize/abstract/24023615/spatio-temporal-environmental-correlation-population-variability
*  The interaction of Nanoarchaeum equitans with Ignicoccus hospitalis: proteins in the contact site between two cells |...
2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci ... Whether this protein, encoded by N. equitans, is involved in protein export or import remains to be determined experimentally. ... The cells were thus preserved in a 'close-to-native' state and permitted a more differentiated view of the contact site. At ... Analysis of archaeal proteins. Cells of I. hospitalis and N. equitans were grown in co-culture as described in [3] under ...
  http://www.biochemsoctrans.org/content/37/1/127
*  Phylogenetic distribution of translational GTPases in bacteria | BMC Genomics | Full Text
267 proteins (from 191 organisms) belong to the EF-Tu family, encoded in 1 to 2 copies of the gene per genome. Most of the ... The gene for CysN/NodQ arose from an archaeal or eukaryotic elongation factor 1 α(EF-1 α) by lateral gene transfer followed by ... where only the core set of genes for the basic processes of gene expression have been preserved. In addition, several other ... Our analysis indicates that 74 genomes code for proteins of the CysN/NodQ subfamily (Figs. 4, 5, 6). In some genomes (Nocardia ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-8-15
*  Viruses and Other Gene Transfer Mechanisms (What'sNEW overflow)
"The team found genes encoding proteins never detected before in bacterial viruses. When in bacteria, these proteins are part of ... "A Selective Barrier to Horizontal Gene Transfer in the T4-Type Bacteriophages That Has Preserved a Core Genome with the Viral ... Martin F. Polz et al., "Horizontal gene transfer and the evolution of bacterial and archaeal population structure" [abstract], ... "Syncytins are 'new' genes encoding the envelope protein of captured endogenous retroviral elements.... These genes are ...
  https://panspermia.org/oldnewvirus.htm