TY  - JOUR
AB  - Background
      		
      			Translation of specific mRNAs can be highly regulated in different cells, tissues or under pathological conditions. Ribosome heterogeneity can originate from variable expression or post-translational modifications of ribosomal proteins. The ribosomal oxygenases RIOX1 (NO66) and RIOX2 (MINA53) modify ribosomal proteins by histidine hydroxylation. A similar mechanism is present in prokaryotes. Thus, ribosome hydroxylation may be a well-conserved regulatory mechanism with implications in disease and development. However, little is known about the evolutionary history of Riox1 and Riox2 genes and their encoded proteins across eukaryotic taxa.
      	
      	
      		
      			Results
      		
      			In this study, we have analysed Riox1 and Riox2 orthologous genes from 49 metazoen species and have constructed phylogenomic trees for both genes. Our genomic and phylogenetic analyses revealed that Arthropoda, Annelida, Nematoda and Mollusca lack the Riox2 gene, although in the early phylum Cnidaria both genes, Riox1 and Riox2, are present and expressed. Riox1 is an intronless single-exon-gene in several species, including humans. In contrast to Riox2, Riox1 is ubiquitously present throughout the animal kingdom suggesting that Riox1 is the phylogenetically older gene from which Riox2 has evolved. Both proteins have maintained a unique protein architecture with conservation of active sites within the JmjC domains, a dimerization domain, and a winged-helix domain. In addition, Riox1 proteins possess a unique N-terminal extension domain. Immunofluorescence analyses in Hela cells and in Hydra vulgaris identified a nucleolar localisation signal within the extended N-terminal domain of human RIOX1 and an altered subnuclear localisation for the Hydra Riox2.
      	
      	
      		
      			Conclusions
      		
      			Conserved active site residues and uniform protein domain architecture suggest a consistent enzymatic activity within the Riox orthologs throughout evolution. However, differences in genomic architecture, like single exon genes and alterations in subnuclear localisation, as described for Hydra, point towards adaption mechanisms that may correlate with taxa- or species-specific requirements. The diversification of Riox1/Riox2 gene structures throughout evolution suggest that functional requirements in expression of protein isoforms and/or subcellular localisation of proteins may have evolved by adaptation to lifestyle.
      	
      
      
      	 
AU  - Bräuer, K.
AU  - Brockers, K.
AU  - Moneer, J.*
AU  - Feuchtinger, A.
AU  - Wollscheid-Lengeling, E.*
AU  - Lengeling, A.*
AU  - Wolf, A.
C1  - 53676
C2  - 44946
CY  - Po Box 211, 1000 Ae Amsterdam, Netherlands
TI  - Phylogenetic and genomic analyses of the ribosomal oxygenases Riox1 (No66) and Riox2 (Mina53) provide new insights into their evolution.
JO  - BMC Evol. Biol.
VL  - 18
IS  - 1
PB  - Elsevier Science Bv
PY  - 2018
ER  - 

TY  - JOUR
AB  - BACKGROUND: Gene duplication is believed to be the classical way to form novel genes, but overprinting may be an important alternative. Overprinting allows entirely novel proteins to evolve de novo, i.e., formerly non-coding open reading frames within functional genes become expressed. Only three cases have been described for Escherichia coli. Here, a fourth example is presented. RESULTS: RNA sequencing revealed an open reading frame weakly transcribed in cow dung, coding for 101 residues and embedded completely in the -2 reading frame of citC in enterohemorrhagic E. coli. This gene is designated novel overlapping gene, nog1. The promoter region fused to gfp exhibits specific activities and 5' rapid amplification of cDNA ends indicated the transcriptional start 40-bp upstream of the start codon. nog1 was strand-specifically arrested in translation by a nonsense mutation silent in citC. This Nog1-mutant showed a phenotype in competitive growth against wild type in the presence of MgCl2. Small differences in metabolite concentrations were also found. Bioinformatic analyses propose Nog1 to be inner membrane-bound and to possess at least one membrane-spanning domain. A phylogenetic analysis suggests that the orphan gene nog1 arose by overprinting after Escherichia/Shigella separated from the other γ-proteobacteria. CONCLUSIONS: Since nog1 is of recent origin, non-essential, short, weakly expressed and only marginally involved in E. coli's central metabolism, we propose that this gene is in an initial stage of evolution. While we present specific experimental evidence for the existence of a fourth overlapping gene in enterohemorrhagic E. coli, we believe that this may be an initial finding only and overlapping genes in bacteria may be more common than is currently assumed by microbiologists.
AU  - Fellner, L.*
AU  - Simon, S.*
AU  - Scherling, C.*
AU  - Witting, M.
AU  - Schober, S.*
AU  - Polte, C.*
AU  - Schmitt-Kopplin, P.
AU  - Keim, D.A.*
AU  - Scherer, S.*
AU  - Neuhaus, K.*
C1  - 47564
C2  - 40679
TI  - Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting.
JO  - BMC Evol. Biol.
VL  - 15
PY  - 2015
ER  - 

TY  - JOUR
AB  - Background: Uncoupling proteins (UCP) are evolutionary conserved mitochondrial carriers that control energy metabolism and therefore play important roles in several physiological processes such as thermogenesis, regulation of reactive oxygen species (ROS), growth control, lipid metabolism and regulation of insulin secretion. Despite their importance in various physiological processes, their molecular function remains controversial. The evolution and phylogenetic distribution may assist to identify their general biological function and structure-function relationships. The exact number of uncoupling protein genes in the fish genome and their evolution is unresolved. Results: Here we report the first characterisation of UCP gene family members in sea bass, Dicentrarchus labrax, and then retrace the evolution of the protein family in vertebrates. Four UCP genes that are shared by five other fish species were identified in sea bass genome. Phylogenetic reconstitution among vertebrate species and synteny analysis revealed that UCP1, UCP2 and UCP3 evolved from duplication events that occurred in the common ancestor of vertebrates, whereas the novel fourth UCP originated specifically in the teleost lineage. Functional divergence analysis among teleost species revealed specific amino acid positions that have been subjected to altered functional constraints after duplications. Conclusions: This work provides the first unambiguous evidence for the presence of a fourth UCP gene in teleost fish genome and brings new insights into the evolutionary history of the gene family. Our results suggest functional divergence among paralogues which might result from long-term and differential selective pressures, and therefore, provide the indication that UCP genes may have diverse physiological functions in teleost fishes. Further experimental analysis of the critical amino acids identified here may provide valuable information on the physiological functions of UCP genes.
AU  - Tine, M.*
AU  - Kuhl, H.*
AU  - Jastroch, M.
AU  - Reinhardt, R.*
C1  - 8639
C2  - 30078
TI  - Genomic characterization of the European sea bass Dicentrarchus labrax reveals the presence of a novel Uncoupling Protein (UCP) gene family member in the teleost fish lineage.
JO  - BMC Evol. Biol.
VL  - 12
IS  - 1
PB  - Biomed Central Ltd.
PY  - 2012
ER  - 

TY  - JOUR
AB  - Background: Teleost fishes of the Coregonidae are good model systems for studying postglacial evolution, adaptive radiation and ecological speciation. Of particular interest is whether the repeated occurrence of sympatric species pairs results from in-situ divergence from a single lineage or from multiple invasions of one or more different lineages. Here, we analysed the genetic structure of Baltic ciscoes (Coregonus albula complex), examining 271 individuals from 8 lakes in northern Germany using 1244 polymorphic AFLP loci. Six lakes had only one population of C. albula while the remaining two lakes had C. albula as well as a sympatric species (C. lucinensis or C. fontanae). Results: AFLP demonstrated a significant population structure (Bayesian theta(B) = 0.22). Lower differentiation between allopatric (theta(B) = 0.028) than sympatric (0.063-0.083) populations contradicts the hypothesis of a sympatric origin of taxa, and there was little evidence for stocking or ongoing hybridization. Genome scans found only three loci that appeared to be under selection in both sympatric population pairs, suggesting a low probability of similar mechanisms of ecological segregation. However, removal of all non-neutral loci decreased the genetic distance between sympatric pairs, suggesting recent adaptive divergence at a few loci. Sympatric pairs in the two lakes were genetically distinct from the six other C. albula populations, suggesting introgression from another lineage may have influenced these two lakes. This was supported by an analysis of isolation-by-distance, where the drift-gene flow equilibrium observed among allopatric populations was disrupted when the sympatric pairs were included. Conclusions: While the population genetic data alone can not unambiguously uncover the mode of speciation, our data indicate that multiple lineages may be responsible for the complex patterns typically observed in Coregonus. Relative differences within and among lakes raises the possibility that multiple lineages may be present in northern Germany, thus understanding the postglacial evolution and speciation in the C. albula complex requires a large-scale phylogenetic analysis of several potential founder lineages.
AU  - Mehner, T.*
AU  - Pohlmann, K.*
AU  - Elkin, C.*
AU  - Monaghan, M.T.*
AU  - Nitz, B.
AU  - Freyhof, J.*
C1  - 6020
C2  - 28115
TI  - Genetic population structure of sympatric and allopatric populations of Baltic ciscoes (Coregonus albula complex, Teleostei, Coregonidae).
JO  - BMC Evol. Biol.
VL  - 10
IS  - 1
PB  - Biomed Central Ltd.
PY  - 2010
ER  - 

TY  - JOUR
AB  - BACKGROUND: The modern wildherd of the tundra muskox (Ovibos moschatus) is native only to the New World (northern North America and Greenland), and its genetic diversity is notably low. However, like several other megafaunal mammals, muskoxen enjoyed a holarctic distribution during the late Pleistocene. To investigate whether collapse in range and loss of diversity might be correlated, we collected mitochondrial sequence data (hypervariable region and cytochrome b) from muskox fossil material recovered from localities in northeastern Asia and the Arctic Archipelago of northern North America, dating from late Pleistocene to late Holocene, and compared our results to existing databases for modern muskoxen. RESULTS: Two classes of haplotypes were detected in the fossil material. "Surviving haplotypes" (SHs), closely similar or identical to haplotypes found in modern muskoxen and ranging in age from approximately 22,000 to approximately 160 yrbp, were found in all New World samples as well as some samples from northeastern Asia. "Extinct haplotypes" (EHs), dating between approximately 44,000 and ~18,000 yrbp, were found only in material from the Taimyr Peninsula and New Siberian Islands in northeastern Asia. EHs were not found in the Holocene muskoxen specimens available for this study, nor have they been found in other studies of extant muskox populations. CONCLUSION: We provisionally interpret this evidence as showing that genetic variability was reduced in muskoxen after the Last Glacial Maximum but before the mid-Holocene, or roughly within the interval 18,000-4,000 yrbp. Narrowing this gap further will require the recovery of more fossils and additional genetic information from this interval.
AU  - MacPhee, R.D.*
AU  - Tikhonov, A.N.*
AU  - Mol, D.*
AU  - Greenwood, A.D.
C1  - 2754
C2  - 23214
TI  - Late quaternary loss of genetic diversity in muskox (Ovibos).
JO  - BMC Evol. Biol.
VL  - 5
PB  - BioMed Central
PY  - 2005
ER  - 

TY  - JOUR
AB  - BACKGROUND: Endogenous retrovirus-like elements (ERV-Ls, primed with tRNA leucine) are a diverse group of reiterated sequences related to foamy viruses and widely distributed among mammals. As shown in previous investigations, in many primates and rodents this class of elements has remained transpositionally active, as reflected by increased copy number and high sequence diversity within and among taxa. RESULTS: Here we examine whether proviral-like sequences may be suitable molecular probes for investigating the phylogeny of groups known to have high element diversity. As a test we characterized ERV-Ls occurring in a sample of extant members of superorder Uranotheria (Asian and African elephants, manatees, and hyraxes). The ERV-L complement in this group is even more diverse than previously suspected, and there is sequence evidence for active expansion, particularly in elephantids. Many of the elements characterized have protein coding potential suggestive of activity. CONCLUSIONS: In general, the evidence supports the hypothesis that the complement had a single origin within basal Uranotheria.
AU  - Greenwood, A.D.
AU  - Engelbrecht, C.C.
AU  - MacPhee, R.D.E.*
C1  - 4105
C2  - 22397
TI  - Characterization of an endogenous retrovirus class in elephants and their relatives.
JO  - BMC Evol. Biol.
VL  - 4
PB  - Biomed Central Ltd
PY  - 2004
ER  -