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PubMed1998

ClpB in a cyanobacterium: predicted structure, phylogenetic relationships, and regulation by light and temperature.

The sequence of a genomic clone encoding a 100-kDa stress protein of Plectonema boryanum (p-ClpB) was determined. The predicted polypeptide contains two putative ATPase regions located within two highly conserved domains (N1 and N2), a spacer region that likely forms a coiled-coil domain, and a highly conserved consensus CK2 phosphorylation domain. The coiled-coil region and the putative site of phosphorylation are not unique to p-ClpB; they are present in all ClpB sequences examined and are absent from the ClpB paralogs ClpA, ClpC, ClpX, and ClpY. Small quantities of a 4.5-kb p-clpB transcript and 110-kDa cytosolic p-ClpB protein were detected in cells grown under optimal conditions; however, increases in the quantities of the transcript and protein were observed in cells grown under excess light and low temperature conditions. Finally, we analyzed ClpA, ClpB, and ClpC sequences from 27 organisms in order to predict phylogenetic relationships among the homologs. We have used this information, along with an identity alignment, to redefine the Clp subfamilies.

Amino Acid Sequence↗
PubMed2004

A description of the Mei2-like protein family; structure, phylogenetic distribution and biological context.

The Schizosaccharomyces pombe Mei2 gene encodes an RNA recognition motif (RRM) protein that stimulates meiosis upon binding a specific non-coding RNA and subsequent accumulation in a "mei2-dot" in the nucleus. We present here the first systematic characterization of the family of proteins with characteristic Mei2-like amino acid sequences. Mei2-like proteins are an ancient eukaryotic protein family with three identifiable RRMs. The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is the most highly conserved of the three RRMs. RRM3 also contains conserved sequence elements at its C-terminus not found in other RRM domains. Single copy Mei2-like genes are present in some fungi, in alveolates such as Paramecium and in the early branching eukaryote Entamoeba histolytica, while plants contain small families of Mei2-like genes. While the C-terminal RRM is highly conserved between plants and fungi, indicating conservation of molecular mechanisms, plant Mei2-like genes have changed biological context to regulate various aspects of developmental pattern formation.

Amino Acid Sequence↗
PubMed2001

Phylogenetic structure of the Sporopachydermia cereana species complex.

A large number of isolates previously referred to as members of the 'Sporopachydermia cereana species complex' were examined by various DNA characterization methods, leading to the conclusion that the complex is in fact made up of 10 species, one of which contains three varieties. The sequences of the internal transcribed spacer (ITS) region and the D1/D2 divergent domains of the large subunit rDNA were determined for representatives of each taxon and specific primers based on differences in the ITS were designed for rapid identification of five of the taxa. Whereas the data provide additional elements for the calibration of the ITS as a criterion for species delineation, the emerging pattern is that the ITS region does not function as well as the D1/D2 domains as an evolutionary clock. Some taxa appear to be specific for the geographical regions where they were isolated, and the distribution of many taxa is mutually exclusive.

Base Composition↗
PubMed2001

Correlation between phylogenetic structure and function: examples from deep-sea Shewanella.

The genus Shewanella is one of the typical deep-sea bacterial genera. Two isolated deep-sea Shewanella species, Shewanella benthica and Shewanella violacea, were found to be able to grow better under high hydrostatic pressure conditions than at atmospheric pressure. These species are not only piezophilic (barophilic), but also psychrophilic. Many psychrophilic and psychrotolerant Shewanella species have been isolated and characterized from cold environments, such as seawater in Antarctica or the North Sea. Some of these cold-adapted Shewanella were shown to be piezotolerant, meaning that growth occurs in a high-pressure habitat. In this review, we propose that two major sub-genus branches of the genus Shewanella should be recognized taxonomically, one group characterized as high-pressure cold-adapted species that produce substantial amounts of eicosapentaenoic acid, and the other group characterized as mesophilic pressure-sensitive species.

Journal Article↗
PubMed2001

Skin test reactivity to mycobacterial antigens parallels the phylogenetic structure of their genus.

SETTING: City of Manaus, Amazonas, Brazil. OBJECTIVE: To explore the relationship between positivity to tuberculin and other environmental mycobacteria sensitins, according to a range of criteria and presence of BCG scar. DESIGN: Dual skin testing with tuberculin and four mycobacterial sensitins, and BCG scar recording of 1070 schoolchildren aged 7-14. Four criteria for positivity were used: simple and dominant, with 5 and 10 mm cut-off points. RESULTS: The standardised prevalence of reactions > or = 5 mm for BCG scar negative children was 58.3% for Mycobacterium avium, 54.2% for M. scrofulaceum, 26.8% for M. fortuitum, 17.9% for M. tuberculosis and 7.6% for M. kansasii. Correlations between tuberculin and each sensitin, for BCG scar negative children, were 0.47 for M. avium, 0.53 for M. scrofulaceum, 0.60 for M. kansasii and 0.22 for M. fortuitum (all with P < 0.01). BCG effect was particularly significant for tuberculin (odds ratio = 3.44 for reactions > or = 5 mm, P < 0.001) and influenced the balance between dominant/non-dominant reactions for all sensitins. CONCLUSION: The correlation between tuberculin and each sensitin confirmed the separation of the rapidly (M. fortuitum) and slowly growing mycobacteria (M. tuberculosis, M. avium, M. scrofulaceum and M. kansasii). The influence of BCG on tuberculin reactions was more marked than on other mycobacterial sensitins.

Adolescent↗
PubMed2004

Methionine adenosyltransferase as a useful molecular systematics tool revealed by phylogenetic and structural analyses.

Structural and phylogenetic relationships among Bacteria and Eukaryota were analyzed by examining 292 methionine adenosyltransferase (MAT) amino acid sequences with respect to the crystal structure of this enzyme established for Escherichia coli and rat liver. Approximately 30% of MAT residues were found to be identical in all species. Five highly conserved amino acid sequence blocks did not vary in the MAT family. We detected specific structural features that correlated with sequence signatures for several clades, allowing taxonomical identification by sequence analysis. In addition, the number of amino acid residues in the loop connecting beta-strands A2 and A3 served to clearly distinguish sequences between eukaryotes and eubacteria. The molecular phylogeny of MAT genes in eukaryotes can be explained in terms of functional diversification coupled to gene duplication or alternative splicing and adaptation through strong structural constraints. Sequence analyses and intron/exon junction positions among nematodes, arthropods and vertebrates support the traditional Coelomata hypothesis. In vertebrates, the liver MAT I isoenzyme has gradually adapted its sequence towards one providing a more specific liver function. MAT phylogeny also served to cluster the major bacterial groups, demonstrating the superior phylogenetic performance of this ubiquitous, housekeeping gene in reconstructing the evolutionary history of distant relatives.

Animals↗
PubMed2001

Phylogenetic and structural analyses of the oxa1 family of protein translocases.

Mitochondrial Oxa1p homologs have been shown to function in protein export and membrane insertion in bacteria, mitochondria and chloroplasts, but their mode of action, organismal distribution and evolutionary origins are poorly understood. All sequenced homologs of Oxa1p were retrieved from the databases and multiply aligned. All organisms with a fully sequenced genome possess at least one Oxa1p homolog showing that the family is truly ubiquitous. Most prokaryotes possess just one Oxa1p homolog, but several Gram-positive bacteria and one archaeon possess two, and eukaryotes may have as many as six. Although these proteins vary in length over a 5-fold range, they exhibit a common hydrophobic core region of about 200 residues. Multiple sequence alignments reveal conserved residues and provide the basis for structural and phylogenetic analyses that serve to characterize the Oxa1 family.

Amino Acid Sequence↗
PubMed2026

treestructure: an R package to detect population structure in phylogenetic trees.

MOTIVATION: How population structure can shape genetic diversity is a longstanding problem in population genetics. While the use of geographic locations, when available, can help answer some of these questions, it is still difficult to determine population structure when such metadata are not available or when the potential population structure is not easily observed. Here, we present an updated version of treestructure, an R package that implements a statistical test based on coalescent theory to detect unobserved population structure in a time-scaled phylogenetic tree. AVAILABILITY: treestructure is available at CRAN at https://cloud.r-project.org/web/packages/treestructure/ and at https://emvolz-phylodynamics.github.io/treestructure/.

Phylogeny↗
PubMed1991

Rat sperm acrosin: cDNA sequence, derived primary structure and phylogenetic origin.

Rat preproacrosin primary structure as predicted from a 1431 nucleotide (nt) cDNA indicates that the molecule is synthesized as a preproenzym consisting of a putative 19 amino acid signal sequence, a 23 amino acid light chain and finally a 395 amino acid heavy chain. Functional domains like the catalytic triad (His-70, Asp-124, Ser-222) are highly conserved not only between the available acrosin primary structures of different mammals but also in comparison with other serine proteinases. Number of amino acid exchanges and the degree in amino acid identity between the different serine proteinases and rat acrosin leads to the assumption that acrosin is one of the early descendants within the phylogenetic tree of the serine proteinase superfamily.

Acrosin↗
PubMed2004

Phylogenetic and structural analysis of mitochondrial complex I proteins.

Our understanding of the evolutionary process would benefit from a better understanding of protein structural changes during evolution. I report that combining phylogenetic and structural analyses of the mitochondrial protein sequences allow to identify important differences between protostomes and deuterostomes mitochondrial proteins: (1) ND5, and with less intensity, ND1, ND2 and ND4, have significantly lower hydrophobicity in deuterostomes than in proterostomes; (2) the C-terminal half portion of ND5 has lower hydrophobicity than the N-terminal half portion, suggesting the presence of larger extra-membrane hydrophilic loops in deuterostomes with respect to protostomes; (3) substitution matrices generated from different complex I proteins show different patterns of amino acid substitutions, suggesting that mitochondrial proteins have different evolutionary dynamics. I hypothesise that the better performances in phylogenetic inference of ND5 with respect to other mitochondrial proteins may be related to its position inside the complex I.

Amino Acid Substitution↗
PubMed1997

Structural and evolutionary studies on sterol 14-demethylase P450 (CYP51), the most conserved P450 monooxygenase: II. Evolutionary analysis of protein and gene structures.

Phylogenetic analyses based on protein sequence data indicated that sterol 14-demethylase P450 (CYP51) and bacterial CYP51-like protein were joined into a distinctive evolutionary cluster, CYP51 cluster, within the CYP protein superfamily. The most probable branch topology of the CYP51 phylogenetic tree was (bacteria, (plants, (fungi, mammals))), which is comparable to the phylogeny of major kingdoms of living matter, suggesting that CYP51 has been conserved from the era of prokaryotic evolution. This may be strong evidence supporting the prokaryotic origin of P450. Structure of flanking regions and the number and insertion sites of introns are quite different between mammalian and fungal CYP51s. This fact indicates that different mechanisms are operative in evolution of protein sequences and gene structures. CYP51 is the first example violating the well-documented rule that the basic structure of a gene, including intron insertion sites, is well conserved in each P450 family. One CYP51 processed a pseudogene was found in rat genome. Nonsynonymous nucleotide divergence observed between the pseudogene and CYP51 cDNA was less than one-fifth of the synonymous divergence. This unusually low rate of nonsynonymous nucleotide changes in the pseudogene suggests that it may be derived from another CYP51, which might have been active for a significant duration in the past.

Amino Acid Sequence↗
PubMed1994

Community structure of a microbial mat: the phylogenetic dimension.

Traditional studies of microbial communities are incomplete because of the inability to identify and quantify all contributing populations. In the present study, we directly determine the abundance and distribution of sulfate-reducing bacterial populations in a microbial mat community by using hybridization probes complementary to the 16S-like rRNAs of major phylogenetic groups. Most of the major groups were found in this single community, distributed for the most part in nonoverlapping depth intervals of the mat. The reflection of the phylogenetic structure in the community structure suggests that those species making up the major phylogenetic groups perform specific interrelated metabolic functions in the community. Comparison of population profiles to previously observed rates of sulfate reduction suggests there are additional populations of sulfate-reducing bacteria both within the photooxic zone and deeper in the mat.

Bacteria↗
PubMed2000

18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, hemiptera).

A secondary structure model for 18S rRNA of peloridiids, relict insects with a present-day circumantarctic distribution, is constructed using comparative sequence analysis, thermodynamic folding, a consensus method using 18S rRNA models of other taxa, and support of helices based on compensatory substitutions. Results show that probable in vivo configuration of 18S rRNA is not predictable using current free-energy models to fold the entire molecule concurrently. This suggests that refinements in free-energy minimization algorithms are needed. Molecular phylogenetic datasets were created using 18S rRNA nucleotide alignments produced by CLUSTAL and rigorous interpretation of homologous position based on certain secondary substructures. Phylogenetic analysis of a hemipteran data matrix of 18S rDNA sequences placed peloridiids sister to Heteroptera. Resolution of affiliations between the three main euhemipteran lineages was unresolved. The peloridiid 18S RNA model presented here provides the most accurate template to date for aligning homologous nucleotides of hemipteran taxa. Using folded 18S rRNA to infer homology of character as morpho-molecular structures or nucleotides and scoring particular sites or substructures is discussed.

Animals↗
PubMed1984

Structure related phylogenetic variations in brain gangliosides of vertebrates.

The concentration and composition of brain gangliosides from five brain structures of vertebrate species belonging to the classes of Chondrichthyes, Osteichthyes, Reptilia, Aves and Mammalia were investigated. The complexity of brain ganglioside composition is strikingly reduced over phyletic lines. In lower vertebrates there is only little variation in the ganglioside pattern between the different brain structures, whereas in higher vertebrates differences distinctly occurred. A similarity over phyletic lines of ganglioside pattern was only noted in phylogenetically old brain structures as for instance in the medulla oblongata and the brain stem.

Animals↗
PubMed1999

Conserved features of Y RNAs revealed by automated phylogenetic secondary structure analysis.

Y RNAs are small 'cytoplasmic' RNAs which are components of the Ro ribonucleoprotein (RNP) complex. The core of this complex, which is found in the cell nuclei of higher eukaryotes as well as the cytoplasm, is composed of a complex between the 60 kDa Ro protein and Y RNAs. Human cells contain four distinct Y RNAs (Y1, Y3, Y4 and Y5), while other eukaryotes contain a variable number of Y RNA homologues. When detected in a particular species, the Ro RNP has been present in every cell type within that particular organism. This characteristic, along with its high conservation among vertebrates, suggests an important function for Ro RNP in cellular metabolism; however, this function has not yet been definitively elucidated. In order to identify conserved features of Y RNA sequences and structures which may be directly involved in Ro RNP function, a phylogenetic comparative analysis of Y RNAs has been performed. Sequences of Y RNA homologues from five vertebrate species have been obtained and, together with previously published Y RNA sequences, used to predict Y RNA secondary structures. A novel RNA secondary structure comparison algorithm, the suboptimal RNA analysis program, has been developed and used in conjunction with available algorithms to find phylogenetically conserved secondary structure models for YI, Y3 and Y4 RNAs. Short, conserved sequences within the Y RNAs have been identified and are invariant among vertebrates, consistent with a direct role for Y RNAs in Ro function. A subset of these are located wholly or partially in looped regions in the Y3 and Y4 RNA predicted model structures, in accord with the possibility that these Y RNAs base pair with other cellular nucleic acids or are sites of interaction between the Ro RNP and other macromolecules.

Animals↗