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Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications

E. V. Koonin, R. L. Tatusov, K. E. Rudd
1995 Proceedings of the National Academy of Sciences of the United States of America  
A computer analysis of 2328 protein sequences comprising about 60% of the Escherichia coli gene products was performed using methods for database screening with individual sequences and alignment blocks  ...  A necessary and complementary approach is the computer analysis of the protein sequences encoded in the genome in order to predict protein functions and derive possible evolutionary relationships.  ...  Our ability to detect sequence conservation is crucial for making functional predictions and evolutionary inferences.  ... 
doi:10.1073/pnas.92.25.11921 pmid:8524875 pmcid:PMC40515 fatcat:b73kxemy5bcwjavnjtikerjwiu

Mitochondrial genomes: anything goes

Gertraud Burger, Michael W Gray, B Franz Lang
2003 Trends in Genetics  
Monophyly: unique origin in a single ancestral species (a monophyletic grouping includes the ancestor and all of its descendants).  ...  Basal (early diverging): emerging early in the evolution of a clade (i.e. a deep branch in a phylogenetic tree).  ...  No correlation is evident in the mode and tempo of evolutionary change in the mitochondrial and nuclear genomes across the broad spectrum of eukaryotic lineages.  ... 
doi:10.1016/j.tig.2003.10.012 pmid:14642752 fatcat:harfjkghkfd4pdntugopvqwk24

Rolling-circle transposons in eukaryotes

V. V. Kapitonov, J. Jurka
2001 Proceedings of the National Academy of Sciences of the United States of America  
This work was supported by National Institutes of Health Grant 2 P41 LM06252-04A1 (to J.J.).  ...  Gabor Toth for helpful discussions and Jolanta Walichiewicz, Dr. Zelek Herman, Alison McCormack, and Michael Jurka for help with editing the manuscript.  ...  Presumably, the 3Ј terminal hairpin, conserved in Helitrons, serves as a terminator of RCR. Evolutionary Implications.  ... 
doi:10.1073/pnas.151269298 pmid:11447285 pmcid:PMC37501 fatcat:wcumyswr35eg7bpqlulnno4mjy

Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis

J. Nosek, M. Novotna, Z. Hlavatovicova, D.W. Ussery, J. Fajkus, L. Tomaska
2004 Molecular Genetics and Genomics  
In contrast to its overall molecular architecture, the coding sequences of the linear mitochondrial DNA of C. parapsilosis are highly similar to their counterparts in the circular mitochondrial genome  ...  The complete sequence has implications for both mitochondrial DNA replication and the evolution of linear DNA genomes.  ...  Minarik (Comenius University, Bratislava) and members of our laboratories for discussions and/or technical assistance. B. F. Lang (University of  ... 
doi:10.1007/s00438-004-1046-0 pmid:15449175 fatcat:z35izxkeonds5pjcprhxsjptam

Strikingly Bacteria-Like and Gene-Rich Mitochondrial Genomes throughout Jakobid Protists

Gertraud Burger, Michael W. Gray, Lise Forget, B. Franz Lang
2013 Genome Biology and Evolution  
Further, protein-coding genes are preceded by potential Shine-Dalgarno translation initiation motifs.  ...  control), and a four-subunit bacteria-like RNA polymerase, which in other eukaryotes is substituted by a nucleus-encoded, single-subunit, phage-like enzyme.  ...  a window on the early evolution of cellular components, biological processes, and molecular functions of the eukaryotic cell.  ... 
doi:10.1093/gbe/evt008 pmid:23335123 pmcid:PMC3590771 fatcat:gjywuq7tkbdmln4svlmi6tlqgm

Evolution of GPCR: Change and continuity

Rainer Strotmann, Kristin Schröck, Iris Böselt, Claudia Stäubert, Andreas Russ, Torsten Schöneberg
2011 Molecular and Cellular Endocrinology  
Their functional diversity is in contrast to the conserved transmembrane core and the invariant set of intracellular signaling mechanisms, and it may be the interplay of these properties that is the key  ...  Once introduced into the very early eukaryotic blueprint, seven-transmembrane receptors soon became the central and versatile components of the evolutionary highly successful G protein-coupled transmembrane  ...  Rhodopsin-like GPCR feature a conserved TM core with typical E/DRY and N/DP(X)nY motifs on the border of TM3 and ICL2 and TM7, respectively, that are present in almost all members of this family (for more  ... 
doi:10.1016/j.mce.2010.07.012 pmid:20708652 fatcat:2p7mpewbnfht3kpdistp3m3fwi

Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging

L. M. Iyer
2004 Nucleic Acids Research  
Elie and F. Constalinesco for their contributions in the early stages of this work and thank P. Forterre and D. D. Leipe for helpful discussions.  ...  In addition, the herA and nurA genes often co-localize with the genes coding for components of the highly conserved DNA repair complex comprised of the archaeal orthologs of the eukaryotic Mre11 (a nuclease  ...  The available information on the functions of the eukaryotic Mre11 and Rad50 proteins provide hints regarding the possible functional significance of the genomic linkage of these four genes.  ... 
doi:10.1093/nar/gkh828 pmid:15466593 pmcid:PMC521647 fatcat:hst63eneuvddlkkphjre4ql5n4

Genome Dynamics in Legionella: The Basis of Versatility and Adaptation to Intracellular Replication

L. Gomez-Valero, C. Buchrieser
2013 Cold Spring Harbor Perspectives in Medicine  
An example is Lpg1684 that codes a protein of unknown function and belongs to the eukaryotic D123 protein family.  ...  AnkY/LegA9/Lpg0402 is also a modular protein as it contains an STPK domain and an ankyrin motif. However, to date, its functional role and putative implication in virulence has not been shown.  ... 
doi:10.1101/cshperspect.a009993 pmid:23732852 pmcid:PMC3662349 fatcat:pr6tloir25d43ivgqnphblghdm

The Genome of the Natural Genetic Engineer Agrobacterium tumefaciens C58

D. W. Wood
2001 Science  
The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists of a circular chromosome, a linear chromosome, and two plasmids.  ...  Extensive orthology and nucleotide colinearity between the genomes of A. tumefaciens and the plant symbiont Sinorhizobium meliloti suggest a recent evolutionary divergence.  ...  The genome contains 5419 predicted protein-coding genes (14) , of which we have assigned a putative function to 3475 (64.1%).  ... 
doi:10.1126/science.1066804 pmid:11743193 fatcat:nov5uw6udrcypcvmhtwkm5ysvm

Expression Patterns of Protein Kinases Correlate with Gene Architecture and Evolutionary Rates

Aleksey Y. Ogurtsov, Leonardo Mariño-Ramírez, Gibbes R. Johnson, David Landsman, Svetlana A. Shabalina, Nikolay A. Spiridonov, Sridhar Hannenhalli
2008 PLoS ONE  
Conclusions/Significance: PK genomic architecture, the size of gene functional domains and evolutionary rates correlate with the pattern of gene expression.  ...  There are considerable differences in genomic organization between PKs up-regulated in the testis and brain.  ...  We thank anonymous reviewers for their helpful comments and suggestions. Author Contributions  ... 
doi:10.1371/journal.pone.0003599 pmid:18974838 pmcid:PMC2572838 fatcat:ebuqks3bffe2lm5gmbpxtiihvi

Genomes: Methanococcus jannaschii and the golden fleece

Roger A. Garrett
1996 Current Biology  
It will have far-reaching consequences for evolutionary studies and for the way in which experimental biology is performed.  ...  The total genome sequence of the archaeon Methanococcus jannaschii completes the trilogy of genomes for the three domains of life -Archaea, Bacteria and Eucarya.  ...  Acknowledgements Discussions with John Reeve and Gary Olsen were much appreciated. My laboratory is supported by the EU genome grant Erbbio4ct960270  ... 
doi:10.1016/s0960-9822(96)00735-x pmid:8939590 fatcat:oxf6wzhavvbrffjhctwrqpmtcq

The code within the code: microRNAs target coding regions

Joshua J. Forman, Hilary A. Coller
2010 Cell Cycle  
In a genome-wide computational screen for functional motifs within coding regions based on evolutionary conservation, highly conserved motifs included some expected motifs, some novel motifs and coding  ...  We also demonstrate a positional bias with greater conservation for sites at the end of the coding region, and the beginning and end of the 3' UTR.  ...  motifs within coding regions based on extreme evolutionary conservation in a multiple species alignment of 17 genomes.2 By quantifying conservation at the DNA sequence level over and above that required  ... 
doi:10.4161/cc.9.8.11202 pmid:20372064 pmcid:PMC2936675 fatcat:canmtjt2rjaglprfswlktnehja

DNA Sequence-Mediated, Evolutionarily Rapid Redistribution of Meiotic Recombination Hotspots

Wayne P. Wahls, Mari K. Davidson
2011 Genetics  
and (B) individual eukaryotes have multiple different DNA sequence motifs that activate hotspots.  ...  Hotspots regulate the position and frequency of Spo11 (Rec12)-initiated meiotic recombination, but paradoxically they are suicidal and are somehow resurrected elsewhere in the genome.  ...  Acknowledgments We thank Reine Protacio for the construction and plating of strains ( Figure 2 ); Giulia Baldini, Jun Gao, Fengling Kan, and Reine Protacio for helpful discussions; Adam Wilkins and anonymous  ... 
doi:10.1534/genetics.111.134130 pmid:22084420 pmcid:PMC3213376 fatcat:ejsxut4fabafvmydvdbixiqhm4

Molecular evolution of NASP and conserved histone H3/H4 transport pathway

Syed Nabeel-Shah, Kanwal Ashraf, Ronald E Pearlman, Jeffrey Fillingham
2014 BMC Evolutionary Biology  
NASP is an essential protein in mammals that functions in histone transport pathways and maintenance of a soluble reservoir of histones H3/H4.  ...  In humans, growing evidence implicates NASP miss-regulation in the development of a variety of cancers.  ...  Clifford Brunk (UCLA) and Dr. Brian Golding (McMaster University) for critically reading the manuscript and providing helpful feedback. We also thank Dr.  ... 
doi:10.1186/1471-2148-14-139 pmid:24951090 pmcid:PMC4082323 fatcat:hsug562d6vdrdgiuxil4reues4

G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae

John A. Capra, Katrin Paeschke, Mona Singh, Virginia A. Zakian, Gary D. Stormo
2010 PLoS Computational Biology  
The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.  ...  We characterized the association of conserved and nonconserved G4 DNA motifs in Saccharomyces cerevisiae with more than 40 known genome features and gene classes.  ...  Acknowledgments We thank Jeannette Carey for teaching KP how to carry out circular dichroism measurements and for the use of her equipment.  ... 
doi:10.1371/journal.pcbi.1000861 pmid:20676380 pmcid:PMC2908698 fatcat:nbrly7iozrezbi6dznc5j5rsqq
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