The evolutionary dynamics of autonomous non-LTR retrotransposons in the lizard Anolis carolinensis shows more similarity to fish than mammals.

The genome of the lizard Anolis carolinensis (the green anole) is the first nonavian reptilian genome sequenced. It offers a unique opportunity to comparatively examine the evolution of amniote genomes. We analyzed the abundance and diversity of non-LTR (long terminal repeat) retrotransposons in the anole using the Genome Parsing Suite. We found that the anole genome contains an extraordinary diversity of elements. We identified 46 families of elements representing five clades (L1, L2, CR1, RTE, and R4). Within most families, elements are very similar to each other suggesting that they have been inserted recently. The rarity of old elements suggests a high rate of turnover, the insertion of new elements being offset by the loss of element-containing loci. Consequently, non-LTR retrotransposons accumulate in the anole at a low rate and are found in low copy number. This pattern of diversity shows some striking similarity with the genome of teleostean fish but contrasts greatly with the low diversity and high copy number of mammalian L1 elements, suggesting a fundamental difference in the way mammals and nonmammalian vertebrates interact with their genomic parasites. The scarcity of divergent elements in anoles suggests that insertions have a deleterious effect and are eliminated by natural selection. We propose that the low abundance of non-LTR retrotransposons in the anole is related directly or indirectly to a higher rate of ectopic recombination in the anole relative to mammals.

Evolution of teleost fish retroviruses: characterization of new retroviruses with cellular genes.

The interactions between retroviruses and their hosts can be of a beneficial or detrimental nature. Some endogenous retroviruses are involved in development, while others cause disease. The Genome Parsing Suite (GPS) is a software tool to track and trace all Retroid agents in any sequenced genome (M. A. McClure et al., Genomics 85:512-523, 2005). Using the GPS, the retroviral content was assessed in four model teleost fish. Eleven new species of fish retroviruses are identified and characterized. The reverse transcriptase protein sequences were used to reconstruct a fish retrovirus phylogeny, thereby, significantly expanding the epsilon-retrovirus family. Most of these novel retroviruses encode additional genes, some of which are homologous to cellular genes that would confer viral advantage. Although the fish divergence is much more ancient, retroviruses began infecting fish genomes approximately 4 million years ago.

Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea.

Although many Archaea have AMP-Acs (acetyl-coenzyme A synthetase) and ADP-Acs, the extant methanogenic genus Methanosarcina is the only identified Archaeal genus that can utilize acetate via acetate kinase (Ack) and phosphotransacetylase (Pta). Despite the importance of ack as the potential urkinase in the ASKHA phosphotransferase superfamily, an origin hypothesis does not exist for the acetate kinase in Bacteria, Archaea, or Eukarya. Here we demonstrate that Archaeal AMP-Acs and ADP-Acs contain paralogous ATPase motifs previously identified in Ack, which demonstrate a novel relation between these proteins in Archaea. The identification of ATPase motif conservation and resulting structural features in AMP- and ADP-acetyl-CoA synthetase proteins in this study expand the ASKHA superfamily to include acetyl-CoA synthetase. Additional phylogenetic analysis showed that Pta and MaeB sequences had a common ancestor, and that the Pta lineage within the halophilc archaea was an ancestral lineage. These results suggested that divergence of a duplicated maeB within an ancient halophilic, archaeal lineage formed a putative pta ancestor. These results provide a potential scenario for the establishment of the Ack/Pta pathway and provide novel insight into the evolution of acetate metabolism for all three domains of life.

Revisiting the evolution of mouse LINE-1 in the genomic era.

BACKGROUND: LINE-1 (L1) is the dominant category of transposable elements in placental mammals. L1 has significantly affected the size and structure of all mammalian genomes and understanding the nature of the interactions between L1 and its mammalian host remains a question of crucial importance in comparative genomics. For this reason, much attention has been dedicated to the evolution of L1. Among the most studied elements is the mouse L1 which has been the subject of a number of studies in the 1980s and 1990s. These seminal studies, performed in the pre-genomic era when only a limited number of L1 sequences were available, have significantly improved our understanding of L1 evolution. Yet, no comprehensive study on the evolution of L1 in mouse has been performed since the completion of this genome sequence. RESULTS: Using the Genome Parsing Suite we performed the first evolutionary analysis of mouse L1 over the entire length of the element. This analysis indicates that the mouse L1 has recruited novel 5'UTR sequences more frequently than previously thought and that the simultaneous activity of non-homologous promoters seems to be one of the conditions for the co-existence of multiple L1 families or lineages. In addition the exchange of genetic information between L1 families is not limited to the 5'UTR as evidence of inter-family recombination was observed in ORF1, ORF2, and the 3'UTR. In contrast to the human L1, there was little evidence of rapid amino-acid replacement in the coiled-coil of ORF1, although this region is structurally unstable. We propose that the structural instability of the coiled-coil domain might be adaptive and that structural changes in this region are selectively equivalent to the rapid evolution at the amino-acid level reported in the human lineage. CONCLUSIONS: The pattern of evolution of L1 in mouse shows some similarity with human suggesting that the nature of the interactions between L1 and its host might be similar in these two species. Yet, some notable differences, particularly in the evolution of ORF1, suggest that the molecular mechanisms involved in host-L1 interactions might be different in these two species.

A bioinformatics approach to the structure, function, and evolution of the nucleoprotein of the order mononegavirales.

The goal of this Bioinformatic study is to investigate sequence conservation in relation to evolutionary function/structure of the nucleoprotein of the order Mononegavirales. In the combined analysis of 63 representative nucleoprotein (N) sequences from four viral families (Bornaviridae, Filoviridae, Rhabdoviridae, and Paramyxoviridae) we predict the regions of protein disorder, intra-residue contact and co-evolving residues. Correlations between location and conservation of predicted regions illustrate a strong division between families while high- lighting conservation within individual families. These results suggest the conserved regions among the nucleoproteins, specifically within Rhabdoviridae and Paramyxoviradae, but also generally among all members of the order, reflect an evolutionary advantage in maintaining these sites for the viral nucleoprotein as part of the transcription/replication machinery. Results indicate conservation for disorder in the C-terminus region of the representative proteins that is important for interacting with the phosphoprotein and the large subunit polymerase during transcription and replication. Additionally, the C-terminus region of the protein preceding the disordered region, is predicted to be important for interacting with the encapsidated genome. Portions of the N-terminus are responsible for N∶N stability and interactions identified by the presence or lack of co-evolving intra-protein contact predictions. The validation of these prediction results by current structural information illustrates the benefits of the Disorder, Intra-residue contact and Compensatory mutation Correlator (DisICC) pipeline as a method for quickly characterizing proteins and providing the most likely residues and regions necessary to target for disruption in viruses that have little structural information available.

Identification of novel retroid agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis.

Retroid agents are genomes that encode a reverse transcriptase (RT) and replicate or transpose by way of an RNA intermediate. The Genome Parsing Suite (GPS) is software created to identify and characterize Retroid agents in any genome database (McClure et al. 2005). The detailed analysis of all Retroid agents found by the GPS in Danio rerio (zebrafish), Oryzias latipes (medaka), Gasterosteus aculeatus (stickleback) and Tetraodon nigroviridis (spotted green pufferfish) reveals extensive Retroid agent diversity in the compact genomes of all four fish. Novel Retroid agents were identified by the GPS software: the telomerase reverse transcriptase (TERT) in O. latipes, G. aculeatus and T. nigroviridis and a potential TERT in D. rerio, a retrotransposon in D. rerio, and multiple lineages of endogenous retroviruses (ERVs) in D. rerio, O. latipes and G. aculeatus.

Automated characterization of potentially active retroid agents in the human genome.

Retroid agents are genomes that encode the reverse transcriptase (RT) and replicate by way of an RNA intermediate. Some retroid agents are implicated in disease via insertional mutagenesis, while others have been found to encode proteins essential to primate reproduction or provide regulatory sequences for host cell processes. The Genome Parsing Suite (GPS), a generic multistep automated process, was developed to characterize all RT-like sequences in the human genome database and to annotate the gene complement of the retroid agents that encode these sequences. In this report the GPS analyzes all significant WU-tBLASTn hits returned for 30 representative RT queries. A total of 128,779 unique RT signals were identified, and 7594 of these were retrieved by RTs not previously reported in the human genome. We have identified 9652 full-length long interspersed nuclear elements (LINEs). Only 159 LINEs are without stop codons or frameshifts.

Potential multiple endonuclease functions and a ribonuclease H encoded in retroposon genomes.

Among the retroposons, the source of the endonuclease activity is known to be variable and can be provided as either a retroviral-like integrase or a protein similar to the cellular apurinic-apyrimidinic endonuclease. It has also been reported that other retroposon and retrointron sequences have limited similarity to various eubacterial endonucleases. We investigated whether any retroposon genomes possibly encode multiple endonuclease functions. Amino acid alignments were generated and analyzed for the presence of the characterized ordered-series-of-motifs (OSM) representative of four different endonuclease functions. The results indicate that SLACS, CZAR, CRE1, CRE2, and some Trypanosoma brucei retroposon sequences encode multiple putative endonuclease functions. Interestingly, one of the endonuclease functions is embedded within the potential ribonuclease H sequence found in SLACS, CZAR, CRE1, CRE2, and R2BM retroposons.

Evidence that the algI/algJ gene cassette, required for O acetylation of Pseudomonas aeruginosa alginate, evolved by lateral gene transfer.

Pseudomonas aeruginosa strains, isolated from chronically infected patients with cystic fibrosis, produce the O-acetylated extracellular polysaccharide, alginate, giving these strains a mucoid phenotype. O acetylation of alginate plays an important role in the ability of mucoid P. aeruginosa to form biofilms and to resist complement-mediated phagocytosis. The O-acetylation process is complex, requiring a protein with seven transmembrane domains (AlgI), a type II membrane protein (AlgJ), and a periplasmic protein (AlgF). The cellular localization of these proteins suggests a model wherein alginate is modified at the polymer level after the transport of O-acetyl groups to the periplasm. Here, we demonstrate that this mechanism for polysaccharide esterification may be common among bacteria, since AlgI homologs linked to type II membrane proteins are found in a variety of gram-positive and gram-negative bacteria. In some cases, genes for these homologs have been incorporated into polysaccharide biosynthetic operons other than for alginate biosynthesis. The phylogenies of AlgI do not correlate with the phylogeny of the host bacteria, based on 16S rRNA analysis. The algI homologs and the gene for their adjacent type II membrane protein present a mosaic pattern of gene arrangement, suggesting that individual components of the multigene cassette, as well as the entire cassette, evolved by lateral gene transfer. AlgJ and the other type II membrane proteins, although more diverged than AlgI, contain conserved motifs, including a motif surrounding a highly conserved histidine residue, which is required for alginate O-acetylation activity by AlgJ. The AlgI homologs also contain an ordered series of motifs that included conserved amino acid residues in the cytoplasmic domain CD-4; the transmembrane domains TM-C, TM-D, and TM-E; and the periplasmic domain PD-3. Site-directed mutagenesis studies were used to identify amino acids important for alginate O-acetylation activity, including those likely required for (i) the interaction of AlgI with the O-acetyl precursor in the cytoplasm, (ii) the export of the O-acetyl group across the cytoplasmic membrane, and (iii) the transfer of the O-acetyl group to a periplasmic protein or to alginate. These results indicate that AlgI belongs to a family of membrane proteins required for modification of polysaccharides and that a mechanism requiring an AlgI homolog and a type II membrane protein has evolved by lateral gene transfer for the esterification of many bacterial extracellular polysaccharides.