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PubMed2005

Comparative genomics and evolution of proteins associated with RNA polymerase II C-terminal domain.

The C-terminal domain (CTD) of the largest subunit of RNA polymerase II provides an anchoring point for a wide variety of proteins involved in mRNA synthesis and processing. Most of what is known about CTD-protein interactions comes from animal and yeast models. The consensus sequence and repetitive structure of the CTD is conserved strongly across a wide range of organisms, implying that the same is true of many of its known functions. In some eukaryotic groups, however, the CTD has been allowed to degenerate, suggesting a comparable lack of essential protein interactions. To date, there has been no comprehensive examination of CTD-related proteins across the eukaryotic domain to determine which of its identified functions are correlated with strong stabilizing selection on CTD structure. Here we report a comparative investigation of genes encoding 50 CTD-associated proteins, identifying putative homologs from 12 completed or nearly completed eukaryotic genomes. The presence of a canonical CTD generally is correlated with the apparent presence and conservation of its known protein partners; however, no clear set of interactions emerges that is invariably linked to conservation of the CTD. General rates of evolution, phylogenetic patterns, and the conservation of modeled tertiary structure of capping enzyme guanylyltransferase (Cgt1) indicate a pattern of coevolution of components of a transcription factory organized around the CTD, presumably driven by common functional constraints. These constraints complicate efforts to determine orthologous gene relationships and can mislead phylogenetic and informatic algorithms.

Amino Acid Sequence↗
PubMed2001

Mammalian play: training for the unexpected.

In this review, we present a new conceptual framework for the study of play behavior, a hitherto puzzling array of seemingly purposeless and unrelated behavioral elements that are recognizable as play throughout the mammalian lineage. Our major new functional hypothesis is that play enables animals to develop flexible kinematic and emotional responses to unexpected events in which they experience a sudden loss of control. Specifically, we propose that play functions to increase the versatility of movements used to recover from sudden shocks such as loss of balance and falling over, and to enhance the ability of animals to cope emotionally with unexpected stressful situations. To obtain this "training for the unexpected," we suggest that animals actively seek and create unexpected situations in play through self-handicapping; that is, deliberately relaxing control over their movements or actively putting themselves into disadvantageous positions and situations. Thus, play is comprised of sequences in which the players switch rapidly between well-controlled movements similar to those used in "serious" behavior and self-handicapping movements that result in temporary loss of control. We propose that this playful switching between in-control and out-of-control elements is cognitively demanding, setting phylogenetic and ontogenetic constraints on play, and is underlain by neuroendocrinological responses that produce a complex emotional state known as "having fun." Furthermore, we propose that play is often prompted by relatively novel or unpredictable stimuli, and is thus related to, although distinct from, exploration. We present 24 predictions that arise from our new theoretical framework, examining the extent to which they are supported by the existing empirical evidence and contrasting them with the predictions of four major alternative hypotheses about play. We argue that our "training for the unexpected" hypothesis can account for some previously puzzling kinematic, structural, motivational, emotional, cognitive, social, ontogenetic, and phylogenetic aspects of play. It may also account for a diversity of individual methods for coping with unexpected misfortunes.

Animals↗
PubMed1995

Toxoplasma gondii comprises three clonal lineages: correlation of parasite genotype with human disease.

The population genetic structure of Toxoplasma gondii was determined by multilocus restriction fragment length polymorphism analysis at 6 loci in 106 independent isolates from humans and animals. Phylogenetic and statistical analyses indicated a highly unusual population structure consisting of 3 widespread clonal lineages. Extensively mixed genotypes were only apparent in 4 strains, which indicated that, while not separate species, sexual recombination between the 3 lineages is exceedingly rare in natural populations. T. gondii is a major cause of subclinical human infection and an important opportunistic pathogen that causes severe disease in immunocompromised patients. While strains from all 3 lineages were isolated from humans, the majority of human toxoplasmosis cases were associated with strains of a type II genotype. The correlation of specific clonal lineages with human toxoplasmosis has important implications for development of vaccines, drug treatments, and diagnostic protocols.

Animals↗
PubMed1996

Thermodynamic prediction of conserved secondary structure: application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein.

An algorithm for prediction of conserved secondary structure of single-stranded RNA is presented. For each RNA of a set of homologous RNAs optimal and suboptimal secondary structures are calculated and stored in a base-pair probability matrix. A multiple sequence alignment is performed for the set of RNAs. The resulting gaps are introduced into the individual probability matrices. These homologous probability matrices are summed to give a consensus probability matrix emphasizing the conserved secondary structure elements of the RNA set. Thus the algorithm combines the advantages of thermodynamic structure prediction by energy minimization with the information obtained from phylogenetic alignment of sequences. The algorithm is applied to three examples. The REV-responsive element of HIV, the structure of which is well known from the literature, was chosen to test the algorithm. The second example is the 3' terminal segment of genomic single-stranded RNAs of cucumber mosaic viruses; a structure similar to that of the related brome mosaic virus was expected and was confirmed. The third example is the prion-protein mRNA from different organisms; the structure of this mRNA is not known. By application of the algorithm highly conserved hairpins were found in the prion-protein mRNA.

Algorithms↗
PubMed1980

Ultrastructural aspects of basal body associated fibrous structures in green algae: a critical review.

Ultrastructural aspects of fibrous structures associated with basal bodies of green algae are critically discussed. It is apparent that variation among these structures is much greater than in microtubular flagellar root systems and it is therefore suggested that fibrous structures may be more useful than microtubular roots in elucidating phylogenetic relationships within the Chlorophyceae sensu Stewart and Mattox and the Prasinophyceae sensu Christensen. Two main types of fibrous structures are distinguished: (1) Connecting fibres (these connect different basal bodies); (2) Fibrous roots (these originate at basal bodies and terminate somewhere else in the cell). Fibrous roots are of two types: (a) microtubular-root associated striated fibres (striation pattern 25-35 nm; system I-fibres); (b) striated fibres composed of a bundle of filaments (filament diameter: 5-10 nm; striation pattern greater than 80 nm; system II fibres). Numbers, disposition and substructure of connecting fibres and fibrious roots are variable in different genera of green algae. In the experimental secretion new observations on fibrous roots in the ulvalean genus Enteromorpha as well as preliminary information on fibrous structures in Carteria obtusa and Bryopsis lyngbyei are included. Functional and evolutionary aspects of fibrous structures associated with the flagellar apparatus of green algae are discussed.

Chlorophyta↗
PubMed2005

Site interdependence attributed to tertiary structure in amino acid sequence evolution.

Standard likelihood-based frameworks in phylogenetics consider the process of evolution of a sequence site by site. Assuming that sites evolve independently greatly simplifies the required calculations. However, this simplification is known to be incorrect in many cases. Here, a computational method that allows for general dependence between sites of a sequence is investigated. Using this method, measures acting as sequence fitness proxies can be considered over a phylogenetic tree. In this work, a set of statistically derived amino acid pairwise potentials, developed in the context of protein threading, is used to account for what we call the structural fitness of a sequence. We describe a model combining statistical potentials with an empirical amino acid substitution matrix. We propose such a combination as a useful way of capturing the complexity of protein evolution. Finally, we outline features of the model using three datasets and show the approach's sensitivity to different tree topologies.

Amino Acid Sequence↗
PubMed2005

ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae).

18S ribosomal DNA and internal transcribed spacer 2 (ITS-2) full-length sequences, each of which was sequenced three times, were used to construct phylogenetic trees with alignments based on secondary structures, in order to elucidate genealogical relationships within the Aplysinidae (Verongida). The first poriferan ITS-2 secondary structures are reported. Altogether 11 Aplysina sponges and 3 additional sponges (Verongula gigantea, Aiolochroia crassa, Smenospongia aurea) from tropical and subtropical oceans were analyzed. Based on these molecular studies, S. aurea, which is currently affiliated with the Dictyoceratida, should be reclassified to the Verongida. Aplysina appears as monophyletic. A soft form of Aplysina lacunosa was separated from other Aplysina and stands at a basal position in both 18S and ITS-2 trees. Based on ITS-2 sequence information, the Aplysina sponges could be distinguished into a single Caribbean-Eastern Pacific cluster and a Mediterranean cluster. The species concept for Aplysina sponges as well as a phylogenetic history with a possibly Tethyan origin is discussed.

Animals↗
PubMed1998

Cloning and expression of an iron-containing superoxide dismutase in the parasitic protist, Trichomonas vaginalis.

A superoxide dismutase (SOD) gene of the parasitic protist Trichomonas vaginalis was cloned, sequenced, expressed in Escherichia coli, and its gene product characterized. It is an iron-containing dimeric protein with a monomeric mass of 22,067 Da. Southern blots analyses suggested the presence of seven iron-containing (FeSOD) gene copies. Hydrophobic cluster analysis revealed some peculiarities in the 2D structure of the FeSOD from T. vaginalis and a strong structural conservation between prokaryotic and eukaryotic FeSODs. Phylogenetic reconstruction of the SOD sequences confirmed the dichotomy between FeSODs and manganese-containing SODs. FeSODs of protists appeared to group together with homologous proteobacterial enzymes suggesting a possible origin of eukaryotic FeSODs through an endosymbiotic event.

Amino Acid Sequence↗
PubMed2003

Enzyme mechanisms for sterol C-methylations.

The mechanisms by which sterol methyl transferases (SMT) transform olefins into structurally different C-methylated products are complex, prompting over 50 years of intense research. Recent enzymological studies, together with the latest discoveries in the fossil record, functional analyses and gene cloning, establish new insights into the enzymatic mechanisms of sterol C-methylation and form a basis for understanding regulation and evolution of the sterol pathway. These studies suggest that SMTs, originated shortly after life appeared on planet earth. SMTs, including those which ultimately give rise to 24 alpha- and 24 beta-alkyl sterols, align the si(beta)-face pi-electrons of the Delta(24)-double bond with the S-methyl group of AdoMet relative to a set of deprotonation bases in the active site. From the orientation of the conformationally flexible side chain in the SMT Michaelis complex, it has been found that either a single product is formed or cationic intermediates are partitioned into multiple olefins. The product structure and stereochemistry of SMT action is phylogenetically distinct and physiologically significant. SMTs control phytosterol homeostasis and their activity is subject to feedback regulation by specific sterol inserts in the membrane. A unified conceptual framework has been formulated in the steric-electric plug model that posits SMT substrate acceptability on the generation of single or double 24-alkylated side chains, which is the basis for binding order, stereospecificity and product diversity in this class of AdoMet-dependent methyl transferase enzymes. The focus of this review is the mechanism of the C-methylation process which, as discussed, can be altered by point mutations in the enzyme to direct the shape of sterol structure to optimize function.

Amino Acid Sequence↗
PubMed2005

[Divergence of the polytene chromosome banding sequences as a reflection of evolutionary rearrangements of the genome linear structure].

Banding sequences of five chromosomal arms (A, C, D, E, and F), accounting for about 70% of the total genome size in 63 Chironomus species, were used as phylogenetic markers to analyze divergence patterns of the linear genome structure during the evolution. The number of chromosomal breakpoints between the pairs of banding sequences compared served as a measure of divergence. It was demonstrated that the greater the divergence between the species compared, the higher the number of chromosomal breakpoints and the smaller the size of the conserved chromosomal regions. A banding sequences comparison in sibling species demonstrated a lower number of chromosomal breakpoints; the breakpoint number was maximum in a comparison of the banding sequences in the subgenera Chironomus and Camptochironomus. The use of the number of chromosomal breakpoints as a divergence measure provided establishment of phylogenetic relationships between 63 Chironomus species and discrimination of sibling species groups and cytocomplexes on a phylogenetic tree.

Animals↗
PubMed1998

NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA.

Many cellular processes involve the preferential interaction of an RNA molecule with a specific protein. A detailed analysis of the individual protein and RNA components of these interactions can provide unique insights into the structural features important for protein-RNA recognition. Ribosomal protein S8 of Escherichia coli plays a key role in 30 S ribosomal subunit assembly through its interaction with 16 S rRNA. The binding site for protein S8 comprises a portion of helix 21, nucleotides G588 to G604 and C634 to C651. This region forms a base-paired helix that is interrupted by a non-Watson-Crick segment composed of nine phylogenetically conserved nucleotides. We have investigated the detailed structure of the conserved segment and the interaction of this region with metal ions using NMR spectroscopy. Twenty-four of the 40 calculated structures converged to similar conformations and were grouped into two families. The main difference between the families is the orientation of the base of U641. The rms deviation between the heavy-atoms of the ten lowest-energy structures is 1.24 A. The orientations of the G597.C643 base-pair and A595.(A596.U644) base-triple within the conserved core have been defined and appear to extend the proximal segment of helix 21 into the phylogenetically conserved core. The base of A642 terminates this helix by stacking against C643 and the base of U641 forms hydrogen bonds with core nucleotides. The conserved core also contains a Mg2+-binding site that promotes stabilization of the secondary and tertiary structure elements of the core. A model for the interaction of S8 with its RNA-binding site is proposed.

Binding Sites↗
PubMed2002

Lyssavirus P gene characterisation provides insights into the phylogeny of the genus and identifies structural similarities and diversity within the encoded phosphoprotein.

A comprehensive phylogenetic analysis of the Lyssavirus genus, employing P gene sequences from 128 isolates recovered globally, is presented. While confirming prior suggestions of the genetic distinctness of the Australian bat lyssaviruses, these data also revealed a clear division within the rabies virus clade (Genotype 1) between globally distributed viruses circulating predominantly in canid species (subgroup 1-1), and American strains harbored by both chiropteran and terrestrial hosts (subgroup 1-2). Nucleotide substitution patterns within the P locus suggested differential selection operating along the length of the open reading frame (ORF) between rabies viruses of these two subgroups. Comparison of the deduced primary sequences of the encoded phosphoproteins of all isolates provided insights into the product's structural organization. Two conserved (CD1,2) and two variable (VD1,2) domains were evident; high variation in the VD2 region was reflected by differences in hydropathic profiles. Only two of five serine residues reported to function as phosphate acceptors in the P protein of the rabies challenge virus standard (CVS) strain were absolutely conserved; similarly, out of four internal methionines reported to direct internal translation initiation of the CVS strain to produce N-terminally truncated P proteins, only Met(20) was universally retained. In contrast, two sequence motifs, one believed to confer binding to the cytoplasmic dynein light chain LC8, and a lysine-rich sequence probably contributing to N protein binding, were conserved throughout the genus. Most rabies viruses of the carnivora (1-1) contain a potential C ORF in alternate frame to that of P, a feature limited or absent in most other isolates of the genus, an observation interpreted with consideration to the predicted course of lyssavirus evolution.

Amino Acid Sequence↗
PubMed1993

Structure of the 16 S ribosomal RNA of the thermophilic cyanobacterium Chlorogloeopsis HTF ('Mastigocladus laminosus HTF') strain PCC7518, and phylogenetic analysis.

The thermophilic cyanobacterial strain, PCC7518, originally identified as 'Mastigocladus laminosus HTF' does not show branchings or heterocysts. The absence of branchings supports the later assignment to the genus Chlorogloeopsis. The absence of heterocysts may be the result of a mutation because heterocysts were observed in the original isolate. Alternatively, contamination may have happened. To solve this problem, the 16 S rRNA sequence was determined and used to infer a secondary structure model and build distance trees. The trees showed that strain PCC7518 belongs to the cluster of heterocystous species and has most probably lost the ability to produce heterocysts by mutation. It is only distantly related to Chlorogloeopsis fritschii PCC6718.

Base Sequence↗
PubMed2003

A new protein structure of P-II class snake venom metalloproteinases: it comprises metalloproteinase and disintegrin domains.

A new metalloproteinase-disintegrin, named Jerdonitin, was purified from Trimeresurus jerdonii venom with a molecular weight of 36 kDa on SDS-PAGE. It dose-dependently inhibited ADP-induced human platelet aggregation with IC(50) of 120nM. cDNA cloning and sequencing revealed that Jerdonitin belonged to the class II of snake venom metalloproteinases (SVMPs) (P-II class). Different from other P-II class SVMPs, metalloproteinase and disintegrin domains of its natural protein were not separated, confirmed by internal peptide sequencing. Compared to other P-II class SVMPs, Jerdonitin has two additional cysteines (Cys219 and Cys238) located in the spacer domain and disintegrin domain, respectively. They probably form a disulfide bond and therefore the metalloproteinase and disintegrin domains cannot be separated by posttranslationally processing. In summary, comparison of the amino acid sequences of Jerdonitin with those of other P-II class SVMPs by sequence alignment and phylogenetic analysis, in conjunction with natural protein structure data, suggested that it was a new type of P-II class SVMPs.

Amino Acid Sequence↗
PubMed2003

Genomic evidence that simian virus 2 and six other simian picornaviruses represent a new genus in Picornaviridae.

Analysis of the VP1 capsid protein coding region of simian virus (SV) 2, SV16, SV18, SV42, SV44, SV45, and SV49 demonstrates that they are clearly distinct from members of the Enterovirus genus and from members of other existing picornavirus genera. To further characterize this group of viruses and to clarify their classification within the Picornaviridae, we have determined the complete genomic sequence of SV2 (8126 nucleotides). The genome was typical of members of Picornaviridae, encoding a single open reading frame. The putative polyprotein contained typical picornavirus protease cleavage sites, yielding mature proteins homologous to each of the known picornavirus proteins. SV2 contained an amino-terminal extension of the reading frame, which was analogous to the leader protein of members of the Aphthovirus, Cardiovirus, Erbovirus, Kobuvirus, and Teschovirus genera, but there was no significant amino acid homology with any of these known leader proteins. The 2A protein also aligned poorly with the 2A proteins of other picornaviruses. The deduced amino acid sequences of the SV2 structural and nonstructural proteins were related to but phylogenetically distinct from those of enteroviruses and human rhinoviruses. The major distinguishing features of SV2 were the presence of a type 2 internal ribosome entry site in the 5'-NTR, a putative leader protein encoded upstream of the structural proteins, and an unusually large 2A protein. On the basis of the molecular analysis, we propose that SV2, SV16, SV18, SV42, SV44, SV45, SV49, and porcine enterovirus 8 be classified as members of a new genus in Picornaviridae and that SV2 (strain 2383) be designated as the type strain.

5' Untranslated Regions↗
PubMed1997

Plant-type ferredoxin-NADP+ reductases: a basal structural framework and a multiplicity of functions.

Ferredoxin-NADP+ (oxido)reductase (EC 1.18.1.2, FNR) is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of this flavoprotein are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. Although ferredoxin-NADP+ reductases have been thoroughly investigated and their properties reviewed on several occasions, considerable advances in the understanding of these flavoenzymes have occurred in the last few years, including the characterization of cDNA and genomic clones encoding FNR proteins from plants, algae, vertebrates, and bacteria, determination of the atomic structure of a plant FNR at high resolution, and the expression of functional reductases in microorganisms like Escherichia coli and Saccharomyces cerevisiae. The aim of this article is to summarize information gained through these recent developments, including the phylogenetic relationships among ferredoxin reductases and the key structural features of the plant FNR family. Other aspects such as the catalytic mechanism of FNR and the molecular events underlying biogenesis, intracellular sorting, folding, and holoenzyme assembly of this important flavoenzyme are also discussed in some detail. Ferredoxin-NADP+ reductases display several outstanding properties that make them excellent model proteins to address broad biological questions.

Bacteria↗
PubMed1993

Unique phylogenetic position of Diplomonadida based on the complete small subunit ribosomal RNA sequence of Giardia ardeae, G. muris, G. duodenalis and Hexamita sp.

Complete small-subunit rRNA (SSU-rRNA) coding region sequences were determined for two species of the intestinal parasite Giardia: G. ardeae and G. muris, both belonging to the order Diplomonadida, and a free-living member of this order, Hexamita sp. These sequences were compared to published SSU-rDNA sequences from a third member of the genus Giardia, G. duodenalis (often called G. intestinalis or G. lamblia) and various representative organisms from other taxa. Of the three Giardia sequences analyzed, the SSU-rRNA from G. muris is the smallest (1432 bases as compared to 1435 and 1453 for G. ardeae and G. duodenalis, respectively) and has the lowest G+C content (58.9%). The Hexamita SSU-rRNA is the largest in this group, containing 1550 bases. Because the sizes of the SSU-rRNA are prokaryotic rather than typically eukaryotic, the secondary structures of the SSU-rRNAs were constructed. These structures show a number of typically eukaryotic signature sequences. Sequence alignments based on constraints imposed by secondary structure were used for construction of a phylogenetic tree for these four taxa. The results show that of the four diplomonads represented, the Giardia species form a distinct group. The other diplomonad Hexamita and the microsporidium Vairimorpha necatrix appear to be distinct from Giardia.

Animals↗
PubMed2002

Phylogeny of phosphoryl transfer proteins of the phosphoenolpyruvate-dependent sugar-transporting phosphotransferase system.

Some bacteria lack sugar permeases of the bacterial phosphotransferase system (PTS) but encode within their genomes phosphoryl transfer proteins of the PTS that probably function in regulation. These proteins include homologues of HPr (PtsH), the ATP-dependent HPr(ser) kinase/phosphatase (PtsK) and the PEP-dependent HPr(his) kinase known as Enzyme I (PtsI). We identify all currently sequenced homologues of these proteins, multiply align their sequences and construct phylogenetic trees in order to derive functional, structural and evolutionary conclusions. We show that no bacterium possesses more than one HPr kinase and that these proteins are probably all orthologous. alpha-Proteobacteria possess truncated HPr kinases which probably serve a unified regulatory function together with other PTS proteins. The Enzymes I are orthologous in all Gram-positive bacteria and some Gram-negative bacteria, but other Gram-negative bacteria exhibit paralogues that fall into 5 functional types. No bacterium with a fully sequenced genome exhibits all of these types. With the exception of the classical Enzymes I, each of these functional types exhibits a distinctive set of accompanying domains, usually with a characteristic domain order. One functional type, the fructose-specific type, includes two phylogenetically different subgroups with different domain orders. The results establish that domain associations occurred early during evolutionary history of the PTS, and that subsequent domain rearrangements occurred rarely. Our findings define the evolutionary histories of these important bacterial proteins and provide guides for functional assignment of PTS-related proteins encoded by genes revealed by genome sequencing.

Amino Acid Sequence↗