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At least 19 recordsLinked to original sources

Muscarinic cholinergic receptor structure. Receptor size, membrane orientation, and absence of major phylogenetic structural diversity.

The structure of the muscarinic acetylcholine receptor was investigated by comparing polypeptides identified by sodium dodecyl sulfate (NaDodSO4)-polyacrylamide gel electrophoresis with the size of the intact receptor in cell membranes as determined by target size analysis. Muscarinic receptors from human, dog, and rat brain, rat and dog cardiac muscle, and guinea pig ileum longitudinal smooth muscle labeled with [3H] propylbenzilylcholine mustard, a covalent affinity reagent, appeared as single polypeptides with molecular weights of 80,000 on NaDodSO4-polyacrylamide gels. NaDodSO4-polyacrylamide gels of ileum smooth muscle muscarinic receptor also consistently displayed smaller peptides of 64, 52, 42, 36, 23, and 18 kDa. In order to determine whether the 80-kDa protein represented all or only a portion of the muscarinic receptor, target size analysis was undertaken. Radiation-induced receptor inactivation was measured by loss of [3H]quinuclidinyl benzilate specific binding and by loss of [3H]propylbenzilylcholine mustard-labeled receptor protein on NaDodSO4 gels. Target size analysis of rat and human brain, canine heart, and guinea pig ileum smooth muscle muscarinic receptors all indicated that the intact membrane-bound receptor has an average molecular mass of 80,000 daltons. These data demonstrate that the protein isolated on NaDodSO4 gels represents the intact receptor molecule. The question of whether structurally distinct receptors exist in different tissues and species was answered, in part, by limited proteolysis studies of the 80-kDa protein isolated from the above tissues. Trypsin and papain produce peptides of 64, 52, 42, 36, 23, and 18 kDa from all receptors studied, indicating a lack of major structural diversity and the absence of multiple structural forms of the muscarinic receptor. Limited proteolysis of the membrane-bound receptor produces a major peptide of 42,000 daltons and minor peptides of 36, 23, and 18 kDa, all of which contain the ligand binding site and protrude from the membrane into the extracellular space.

Animals↗

Phylogenetic structure of the prokaryotic domain: the primary kingdoms.

A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: (i) the eubacteria, comprising all typical bacteria; (ii) the archaebacteria, containing methanogenic bacteria; and (iii) the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells.

Bacteria↗

Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization.

The phylogenetic relationships of 49 Acinetobacter strains, 46 of which have previously been classified into 18 genomic species by DNA-DNA hybridization studies, were investigated using the nucleotide sequence of gyrB, the structural gene for the DNA gyrase B subunit. The phylogenetic tree showed linkages between genomic species 1 (Acinetobacter calcoaceticus), 2 (Acinetobacter baumannii), 3 and TU13; genomic species 6, BJ15, BJ16 and BJ17; genomic species 5, BJ13 (synonym of TU14) and BJ14; genomic species 7 (Acinetobacter johnsonii), 10 and 11; and genomic species 8 and 9. The phylogenetic grouping of Acinetobacter strains based on gyrB genes was almost congruent with that based on DNA-DNA hybridization studies. Consequently, gyrB sequence comparison can be used to resolve the taxonomic positions of bacterial strains at the level of genomic species. However, minor discrepancies existed in the grouping of strains of genomic species 8, 9 and BJ17. The phylogenetic tree for these strains was reconstructed from the sequence of rpoD, the structural gene for the RNA polymerase sigma 70 factor. The latter tree was 100% congruent with the grouping based on DNA-DNA hybridization. The reliability of DNA-DNA hybridization may be superior to that of sequence comparison of a single protein-encoding gene in resolving closely related organisms since the former method measures the homologies between the nucleotide sequences of total genomic DNAs. Three strains that have not been characterized previously by DNA-DNA hybridization seem to belong to two new genomic species, one including strain ATCC 33308 and the other including strains ATCC 31012 and MBIC 1332.

Acinetobacter↗

Phylogenetic structure in the grass family (Poaceae): evidence from the nuclear gene phytochrome B.

Phylogenetic analyses of partial phytochrome B (PHYB) nuclear DNA sequences provide unambiguous resolution of evolutionary relationships within Poaceae. Analysis of PHYB nucleotides from 51 taxa representing seven traditionally recognized subfamilies clearly distinguishes three early-diverging herbaceous "bambusoid" lineages. First and most basal are Anomochloa and Streptochaeta, second is Pharus, and third is Puelia. The remaining grasses occur in two principal, highly supported clades. The first comprises bambusoid, oryzoid, and pooid genera (the BOP clade); the second comprises panicoid, arundinoid, chloridoid, and centothecoid genera (the PACC clade). The PHYB phylogeny is the first nuclear gene tree to address comprehensively phylogenetic relationships among grasses. It corroborates several inferences made from chloroplast gene trees, including the PACC clade, and the basal position of the herbaceous bamboos Anomochloa, Streptochaeta, and Pharus. However, the clear resolution of the sister group relationship among bambusoids, oryzoids, and pooids in the PHYB tree is novel; the relationship is only weakly supported in ndhF trees and is nonexistent in rbcL and plastid restriction site trees. Nuclear PHYB data support Anomochlooideae, Pharoideae, Pooideae sensu lato, Oryzoideae, Panicoideae, and Chloridoideae, and concur in the polyphyly of both Arundinoideae and Bambusoideae.

Journal Article↗

Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees.

Because of the correlation expected between the phylogenetic relatedness of two taxa and their net ecological similarity, a measure of the overall phylogenetic relatedness of a community of interacting organisms can be used to investigate the contemporary ecological processes that structure community composition. I describe two indices that use the number of nodes that separate taxa on a phylogeny as a measure of their phylogenetic relatedness. As an example of the use of these indices in community analysis, I compared the mean observed net relatedness of trees (≥10 cm diameter at breast height) in each of 28 plots (each 0.16 ha) in a Bornean rain forest with the net relatedness expected if species were drawn randomly from the species pool (of the 324 species in the 28 plots), using a supertree that I assembled from published sources. I found that the species in plots were more phylogenetically related than expected by chance, a result that was insensitive to various modifications to the basic methodology. I tentatively infer that variation in habitat among plots causes ecologically more similar species to co-occur within plots. Finally, I suggest a range of applications for phylogenetic relatedness measures in community analysis.

net ecological similarity↗

Phylogenetic, structural and functional analyses of the LacI-GalR family of bacterial transcription factors.

Phylogenetic tree construction for 25 sequenced members of the LacI-GalR family (LGF) of transcription factors revealed that almost all branches are similar in length, radiating essentially from a single point. This observation suggests that most of these proteins arose by duplication events which occurred at a specific time in evolutionary history, and that further duplication events were rare. Analyses of the multiple alignment of the LGF proteins lead to suggestions regarding structure-function relationships and reveal that the helix-turn-helix DNA-binding motif of LGF proteins is similar in sequence to those of numerous non-homologous DNA-binding proteins.

Amino Acid Sequence↗

The 16S-like, 5.8S and 23S-like rRNAs of the two varieties of Cryptococcus neoformans: sequence, secondary structure, phylogenetic analysis and restriction fragment polymorphisms.

The nucleotide sequences of the 16S-like, 5.8S and 23S-like rDNAs from the two varieties of Cryptococcus neoformans, C. neoformans var. neoformans and C. neoformans var. gattii, were determined. The rRNA locus has the typical eukaryote organization of 16S-5.8S-23S with the 16S-like and 5.8S rRNA genes separated by a 124-nucleotide spacer and the 5.8S and 23S-like rRNA genes separated by a 187-nucleotide spacer in each strain. The C. neoformans var. neoformans and C. neoformans var. gattii 16S-like, 5.8S and 23S-like rRNAs are, respectively 1802, 158, and 3358 nucleotides in length and share > 99% nucleotide sequence identity, a finding which strongly supports the present taxonomic classification of two varieties within a species. Comparative structure analysis was used to construct secondary-structure models for the deduced 16S-like and 5.8S-23S-like rRNA sequences, which are similar to those of other fungal rRNAs. The C. neoformans 16S-like and 23S-like rRNA sequences were aligned with other eukaryote sequences based on secondary and higher-order structures predicted by comparative structure analysis for phylogenetic analysis. There was good correspondence between the 16S-like and 23S-like derived phylogenetic trees. The closest known fungal relative is Trichosporon beigelii. Southern blot analysis revealed one C. neoformans strain with two types of DNA repeats coding for rRNA which differed in size by about 1000 bp. Restriction fragment length polymorphisms in the rDNA locus provide useful markers for the study of epidemiology and pathogenesis of C. neoformans infections.

Base Sequence↗

The phylogenetic structure of the genus Acinetobacter.

16S rDNA sequence analysis was performed on the type strains of all validly described Acinetobacter species and five unnamed Acinetobacter strains. The phylogenetic analyses confirm that Acinetobacter is a coherent genus within the gamma subclass of Proteobacteria and that the species are phylogenetically well defined. A. calcoaceticus, A. lwoffii, A. johnsonii and A. haemolyticus form one cluster of closely related species, the pair A. junii and A. baumannii forms a second cluster. A. radioresistens stands phylogenetically isolated. The study reveals that three undescribed strains can be assigned to individually described species, while strains DSM 30009 and DSM 590 may represent two novel Acinetobacter species.

Acinetobacter↗

A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages.

The aims of the work were (1) to develop statistical tests to identify whether substitution takes place under a covariotide model in sequences used for phylogenetic inference and (2) to determine the influence of covariotide substitution on phylogenetic trees inferred for photosynthetic and other organisms. (Covariotide and covarion models are ones in which sites that are variable in some parts of the underlying tree are invariable in others and vice versa.) Two tests were developed. The first was a contingency test, and the second was an inequality test comparing the expected number of variable sites in two groups with the observed number. Application of these tests to 16S rDNA and tufA sequences from a range of nonphotosynthetic prokaryotes and oxygenic photosynthetic prokaryotes and eukaryotes suggests the occurrence of a covariotide mechanism. The degree of support for partitioning of taxa in reconstructed trees involving these organisms was determined in the presence or absence of sites showing particular substitution patterns. This analysis showed that the support for splits between (1) photosynthetic eukaryotes and prokaryotes and (2) photosynthetic and nonphotosynthetic organisms could be accounted for by patterns arising from covariotide substitution. We show that the additional problem of compositional bias in sequence data needs to be considered in the context of patterns of covariotide/covarion substitution. We argue that while covariotide or covarion substitution may give rise to phylogenetically informative patterns in sequence data, this may not always be so.

Markov Chains↗

Phylogenetic, structural and functional characteristics of the Na-K-Cl cotransporter family.

Bumetanide-sensitive Na-K-Cl cotransporters and thiazide-sensitive Na-Cl cotransporters comprise a family of integral membrane transport proteins, the Na-K-Cl cotransporter (NKCC) family. Each of the members of this family is over 1,000 amino acids in length. We have multiply aligned the ten currently sequenced members of this family from human, rabbit, rodent, shark, flounder, moth, worm and yeast sources. Phylogenetic analyses suggest the presence of at least six isoforms of these full length proteins in eukaryotes. Average hydropathy and average similarity plots have been derived revealing that each of these proteins possesses a central, well conserved, hydrophobic domain of almost invariant length, possibly consisting of twelve transmembrane alpha-helical spanners, an N-terminal, poorly conserved, hydrophilic domain of variable length, and a C-terminal, moderately conserved, hydrophilic domain of moderately constant length. A functionally uncharacterized homologue of this family occurs in the cyanobacterium Synechococcus sp. Limited sequence similarity of these proteins with members of a family of basic amino acid transporters suggest that the NKCC family may be distantly related to the previously characterized, ubiquitous, amino acid-polyamine-choline (APC) family of facilitators. These observations suggest that the NKCC family is an old family that has its roots in the prokaryotic kingdom.

Amino Acid Sequence↗

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↗

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↗

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↗

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↗

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↗