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PubMed2005

Phylogenetic and exon-intron structure analysis of fungal subtilisins: support for a mixed model of intron evolution.

Phylogenetic and exon-intron structure analyses of intra- and interspecific fungal subtilisins in this study provided support for a mixed model of intron evolution: a synthetic theory of introns-early and introns-late speculations. Intraspecifically, there were three phase zero introns in Pr1A and its introns 1 and 2 located at the highly conserved positions were phylogentically congruent with coding region, which is in favor of the view of introns-early speculation, while intron 3 had two different sizes and was evolutionarily incongruent with coding region, the evidence for introns-late speculation. Noticeably, the subtilisin Pr1J gene from different strains of M. ansiopliae contained different number of introns, the strong evidence in support of introns-late theory. Interspecifically, phylogenetic analysis of 60 retrievable fungal subtilisins provided a clear relationship between amino acid sequence and gene exon-intron structure that the homogeneous sequences usually have a similar exon-infron structure. There were 10 intron positions inserted by highly biased phase zero introns across examined fungal subtilisin genes, half of these positions were highly conserved, while the others were species-specific, appearing to be of recent origins due to intron insertion, in favor of the introns-late theory. High conservations of positions 1 and 2 inserted by the high percentage of phase zero introns as well as the evidence of phylogenetic congruence between the evolutionary histories of intron sequences and coding region suggested that the introns at these two positions were primordial.

Amino Acid Sequence↗
PubMed1998

Endonucleolytic cleavage of RNA at 5' endogenous stem structures by human flap endonuclease 1.

Structure-specific nucleases called 5' flap endonucleases cleave unannealed 5' arms of template-primer DNA model substrates at the start of the duplex and are involved in Okazaki fragment processing during DNA synthesis. To determine the possible use of the enzymes in RNA structure analysis, the cleavage of synthetic and native RNAs was examined using flap endonuclease 1 (Fen1) of HeLa cells. RNAs are cleaved at about 20% of the rate of DNA model substrates, and most of the cleavage sites are within 200 nucleotides of the 5' end. Hydrolysis of MFA2 mRNA of yeast shows that the cleavages are at the start of five possible stem structures of a folded secondary structure predicted on the basis of both chemical and enzymatic structure probing. 16S ribosomal RNA of Escherichia coli is cleaved at several 5' stem structures of its phylogenetically predicted folded structure. This type of RNA cleavage specificity may be very useful in secondary structure analysis in the future and also may be used by cells for specific 5' end-geared RNA cleavages.

Base Sequence↗
PubMed1995

Secondary structures of Escherichia coli antisense micF RNA, the 5'-end of the target ompF mRNA, and the RNA/RNA duplex.

The Escherichia coli micF RNA is a prototype for a class of antisense RNAs encoded by genes at different loci from those that code for their target RNAs. RNAs in this class exhibit only partial complementarity to their targets. micF RNA binds to and regulates the stability of ompF mRNA in response to a variety of environmental stimuli. The secondary structures of micF RNA, ompF-213 mRNA (a segment containing the 213 nucleotides at the 5'-terminus of the target message), and the micF RNA/ompF-213 mRNA duplex were analyzed in vitro by partial digestion with structure-specific ribonucleases and chemical modification. Both micF RNA and ompF mRNA have single-stranded 5'-ends and contain stable stem-loop structures. Strong phylogenetic support for the proposed secondary structure for E. coli micF RNA is provided by a comparison of structural models derived from micF sequences from related bacteria. The micF RNA/ompF-213 mRNA duplex interaction appears to involve only a short segment of micF RNA. Unfolding of only one stem-loop of micF RNA and a minor stem-loop of ompF-213 mRNA appears to be necessary to form the duplex. The probing data suggest that the Shine-Dalgarno sequence and AUG start codon of ompF mRNA, found in single-stranded regions in the free message, are base-paired to micF RNA in the RNA/RNA duplex.

Bacterial Outer Membrane Proteins↗
PubMed1999

A Boltzmann filter improves the prediction of RNA folding pathways in a massively parallel genetic algorithm.

RNA folding using the massively parallel genetic algorithm (GA) has been enhanced by the addition of a Boltzmann filter. The filter uses the Boltzmann probability distribution in conjunction with Metropolis' relaxation algorithm. The combination of these two concepts within the GA's massively parallel computational environment helps guide the genetic algorithm to more accurately reflect RNA folding pathways and thus final solution structures. Helical regions (base-paired stems) now form in the structures based upon the stochastic properties of the thermodynamic parameters that have been determined from experiments. Thus, structural changes occur based upon the relative energetic impact that the change causes rather than just geometric conflicts alone. As a result, when comparing the predictions to phylogenetically determined structures, over multiple runs, fewer false-positive stems (predicted incorrectly) and more true-positive stems (predicted correctly) are generated, and the total number of predicted stems representing a solution is diminished. In addition, the significance (rate of occurrence) of the true-positive stems is increased. Thus, the predicted results more accurately reflect phylogenetically determined structures.

Algorithms↗
PubMed2003

First complete large subunit ribosomal RNA sequence and secondary structure for a parasitic nematode: phylogenetic and diagnostic implications.

The complete sequence and secondary structure of the large subunit of nuclear ribosomal RNA(LSUrRNA) were determined for the parasitic nematode Labiostrongylus bipapillosus (order Strongylida). Its LSU rRNA sequence was shorter (by 18 bp) than that of the free-living nematode, Caenorhabditis elegans (order Rhabditida), the only other species within the Nematoda for which a complete LSU rRNA sequence has been determined. Interspecific differences in sequence were greater in the 12 D domains compared with the core segments, with the secondary structure being maintained by partial or complete compensatory base pair changes. The magnitude of interspecific sequence difference in each D domain (except for D6 and D12) was similar, suggesting that several domains contain informative genetic markers for phylogenetic studies of the phylum Nematoda at different taxonomic levels. The LSU rRNA may also provide species-specific markers for the identification of some bursate nematodes of veterinary and medical importance.

Animals↗
PubMed1998

Phylogenetic analysis and intrageneric structure of the genus Hyphomicrobium and the related genus Filomicrobium.

Almost complete 16S rDNA sequences from the type strains of seven species of the genus Hyphomicrobium and of Filomicrobium fusiforme have been determined. The Hyphomicrobium species from two phylogenetic clusters that are only moderately related to each other. While cluster I contains the type species Hyphomicrobium vulgare, Hyphomicrobium aestuarii, Hyphomicrobium hollandicum and Hyphomicrobium zavarzinii, cluster II comprises Hyphomicrobium facilis, Hyphomicrobium denitrificans and Hyphomicrobium methylovorum. Within the two species cluster, the species are highly related. Phylogenetically, Filomicrobium fusiforme clusters moderately with Hyphomicrobium species. The lack of distinguishing phenotypical properties presently excludes the possibility of describing cluster II as a new genus.

Base Sequence↗
PubMed1991

Phylogenetic comparative analysis of RNA structure on Macintosh computers.

A Macintosh Hypertalk program (Hypercard 'stack') for use in phylogenetic comparative analysis of RNA structure is described. The program identifies covariations and compensatory changes in RNA sequence alignments, for use in the construction of secondary structure models or the identification of tertiary interactions. The results of an analysis are presented either as a list of positions in the alignment which covary, or as a 2-dimensional matrix in which potential helices in the secondary structure appear as diagonal patterns.

Microcomputers↗
PubMed2007

Cytochrome c(2) Exit Strategy: Dissociation Studies and Evolutionary Implications.

Small, water-soluble, type c cytochromes form a transient network connecting major bioenergetic membrane protein complexes in both photosynthesis and respiration. In the photosynthesis cycle of Rhodobacter sphaeroides, cytochrome c2 (cyt c2) docks to the reaction center (RC), undergoes electron transfer, and exits for the cytochrome bc1 complex. Translations of cyt c2 about the RC-cyt c2 docking interface and surrounding membrane reveal possible exit pathways. A pathway at a minimal elevation allowed by the architecture of the RC is analyzed using both an all-atom steered molecular dynamics simulation of the RC-cyt c2 complex and a bioinformatic analysis of the structures and sequences of cyt c. The structure-based phylogenetic analysis allows for the identification of structural elements that have evolved to satisfy the requirements of having multiple functional partners. The patterns of evolutionary variation obtained from the phylogenetic analysis of both docking partners of cyt c2 reveal conservation of key residues involved in the interaction interfaces that would be candidates for further experimental studies. Additionally, using the molecular mechanics Poisson-Boltzmann surface area method we calculate that the binding free energy of reduced cyt c2 to the RC is nearly 6 kcal/mol more favorable than with oxidized cyt c2. The redox-dependent variations lead to changes in structural flexibility, behavior of the interfacial water molecules, and eventually changes in the binding free energy of the complex.

Amino Acid Sequence↗
PubMed1999

Organization of the chromosomal region containing the genes lexA and topA in Thermotoga neapolitana. Primary structure of LexA reveals phylogenetic relevance.

The chromosomal region of Thermotoga neapolitana surrounding the gene lexA (4283 bp) was sequenced. In addition to the topoisomerase gene top2A it contained five open reading frames. A part of the cloned region showed high sequence homology with a previously published sequence of Th. maritima and indicated an identical arrangement of genes in both microorganisms. Structural analysis of the LexA protein showed significant, but relatively low overall homology with LexA proteins of other bacteria, especially in the DNA binding region. However, key amino acids for processing and secondary structure elements like the helix-turn-helix motif are well conserved. Sequence alignment analysis of the whole protein and the DNA-binding sites of all known LexA sequences uncovers groups of similarity reminding the phylogenetic tree of the Bacteria. A consensus sequence with the SOS- or Cheo-box upstream of the lexA gene of Th. maritima and Th. neapolitana was absent. Together with the phylogenetic distance of the Thermotogales from other bacteria this suggests the presence of a new operator target sequence specific for the Thermotogales, in analogy to the SOS-box for the gamma-group Proteobacteria and the Cheo-box for low- and high-GC Gram-positive bacteria.

Amino Acid Sequence↗
PubMed1996

Mycoplasma fermentans simplifies our view of the catalytic core of ribonuclease P RNA.

The catalytic RNA moiety of (eu)bacterial RNase P is responsible for cleavage of the 5' leader sequence from precursor tRNAs. We report the sequence, the catalytic properties, and a phylogenetic-comparative structural analysis of the RNase P RNA from Mycoplasma fermentans, at 276 nt the smallest known RNase P RNA. This RNA is noteworthy in that it lacks a stem-loop structure (helix P12) that was thought previously to be universally present in bacterial RNase P RNAs. This finding suggests that helix P12 is not required for catalytic activity in vivo. In order to test this possibility in vitro, the kinetic properties of M. fermentans RNase P RNA and a mutant Escherichia coli RNase P RNA that was engineered to lack helix P12 were determined. These RNase P RNAs are catalytically active with efficiencies (Kcat/Km) comparable to that of native E. coli RNase P RNA. These results show that helix P12 is dispensable in vivo in some organisms, and therefore is unlikely to be essential for the mechanism of RNase P action. The notion that all phylogenetically volatile structures in RNase P RNA are dispensable for the catalytic mechanism was tested. A synthetic RNA representing the phylogenetic minimum RNase P RNA was constructed by deleting all evolutionarily variable structures from the M. fermentans RNA. This simplified RNA (Micro P RNA) was catalytically active in vitro with approximately 600-fold decrease in catalytic efficiency relative to the native RNA.

Base Sequence↗
PubMed2002

Protein-translocating outer membrane porins of Gram-negative bacteria.

Five families of outer membrane porins that function in protein secretion in Gram-negative bacteria are currently recognized. In this report, these five porin families are analyzed from structural and phylogenetic standpoints. They are the fimbrial usher protein (FUP), outer membrane factor (OMF), autotransporter (AT), two-partner secretion (TPS) and outer membrane secretin (Secretin) families. All members of these families in the current databases were identified, and all full-length homologues were multiply aligned for structural and phylogenetic analyses. The organismal distribution of homologues in each family proved to be unique with some families being restricted to proteobacteria and others being widespread in other bacterial kingdoms as well as eukaryotes. The compositions of and size differences between subfamilies provide evidence for specific orthologous relationships, which agree with available functional information and intra-subfamily phylogeny. The results reveal that horizontal transfer of genes encoding these proteins between phylogenetically distant organisms has been exceptionally rare although transfer within select bacterial kingdoms may have occurred. The resultant in silico analyses are correlated with available experimental evidence to formulate models relevant to the structures and evolutionary origins of these proteins.

Consensus Sequence↗
PubMed1997

The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants.

Sequences of the Internal Transcribed Spacer 2 (ITS-2) regions of the nuclear rDNA repeats from 111 organisms of the family Volvocaceae (Chlorophyta) and unicellular organisms of the Volvocales, including Chlamydomonas reinhardtii, were determined. The use of thermodynamic energy optimization to generate secondary structures and phylogenetic comparative analysis of the spacer regions revealed a common secondary structure that is conserved despite wide intra- and interfamilial primary sequence divergence. The existence of this conserved higher-order structure is supported by the presence of numerous compensating basepair changes as well as by an evolutionary history of insertions and deletions that nevertheless maintains major aspects of the overall structure. Furthermore, this general structure is preserved across broad phylogenetic lines, as it is observed in the ITS-2s of other chlorophytes, including flowering plants; previous reports of common ITS-2 secondary structures in other eukaryotes were restricted to the order level. The reported ITS-2 structure possesses important conserved structural motifs which may help to mediate cleavages in the ITS-2 that occur during rRNA transcript processing. Their recognition can guide further studies of eukaryotic rRNA processing, and their application to sequence alignments may contribute significantly to the value of ITS-2 sequences in phylogenetic analyses at several taxonomic levels, but particularly in characterizing populations and species.

Base Sequence↗
PubMed1995

The computer simulation of RNA folding pathways using a genetic algorithm.

A procedure for simulating the RNA folding process using the principles of genetic algorithm is proposed. The method allows one to simulate a folding pathway of RNA, including such processes as disruption of temporarily formed structures, the folding of a molecule during its synthesis and pseudoknot formation. The simulations are able to predict functional metastable foldings and kinetically driven transitions to more stable structures. The analysis of free energies for intermediate foldings allows estimation of the ranges of kinetic refolding barriers and suggests that in some RNAs the selective evolutionary pressure suppresses the possibilities for alternative structures that could form in the course of transcription. It is shown that the folding pathway simulation can result in structure predictions that are more consistent with phylogenetically proven structures than minimum energy solutions. This suggest that RNA folding kinetics is very important for the formation of functional RNA structures. Therefore, apart form its value for predictions of RNA structures, the proposed computer simulations can be a powerful tool in the studies of RNA folding features.

Algorithms↗
PubMed1967

The distribution of cytochrome-oxidase activity in rabbit brain.

1. The cytochrome-oxidase activity in eleven structures of the rabbit brain has been investigated. 2. Kinetic data suggest that the same enzyme occurs in all brain structures but that the activity on a tissue-weight basis differs from structure to structure, being in general higher in the phylogenetically newer structures. 3. When the kinetic data are related to cell density (as measured by DNA concentration) all the neuron-containing structures of the cerebrum and brain stem show the same activity but the corpus callosum and the cerebellum show much less. 4. A special study was made of the distribution of activity and cell density within the diencephalon. 5. The results suggest that all neurons in the cerebrum and brain stem have a similar cytochrome-oxidase activity, which is about 80 times that of glia, and that the cerebellum is relatively richer in glia or that it contains neurons with a much lower cytochrome-oxidase activity, or both.

Animals↗
PubMed1995

Rat mammary-gland transferrin: nucleotide sequence, phylogenetic analysis and glycan structure.

The complete cDNA for rat mammary-gland transferrin (Tf) has been sequenced and also the native protein isolated from milk in order to analyse the structure of the main glycan variants present. A lactating-rat mammary-gland cDNA library in lambda gt10 was screened with a partial cDNA copy of rat liver Tf and subsequently rescreened with 5' fragments of the longest clones. This produced a 2275 bp insert coding for an open reading frame of 695 amino acid residues. This includes a 19-amino acid signal sequence and the mature protein containing 676 amino acids and one N-glycosylation site in the C-terminal domain at residue 490. Phylogenetic analysis was carried out using 14 translated Tf nucleotide sequences, and the derived evolutionary tree shows that at least three gene duplication events have occurred during Tf evolution, one of which generated the N- and C-terminal domains and occurred before separation of arthropods and chordates. The two halves of human melanotransferrin are more similar to each other than to any other sequence, which contrasts with the pattern shown by the remaining sequences. Native rat milk Tf is separated into four bands on native PAGE that differ only in their sialic acid content: one biantennary glycan is present containing either no sialic acid residues or up to three. The complete structures of the two major variants were determined by methylation, m.s. and 400 MHz 1H-n.m.r. spectroscopy. They contain either one or two neuraminic acid residues (alpha 2-->6)-linked to galactose in conventional biantennary N-acetyl-lactosamine-type glycans. Most contain fucose (alpha 1-->6)-linked to the terminal non-reducing N-acetylglucosamine.

Animal Population Groups↗
PubMed2003

Structure, genomic organization, and phylogenetic implications of six new VH families in the channel catfish.

To define members of previously unknown VH gene families, a channel catfish immunoglobulin heavy chain cDNA library was constructed and screened with probes specific for the seven known catfish VH families. Reiterative screening and sequence studies defined six new VH families, designated VH8-VH13, which brings the total number of VH families in the catfish to 13. This is the highest number of VH families presently defined in a lower vertebrate. Sequence comparisons indicate there is extensive diversity between members of different families with the greatest variability encoded within the complementarity determining regions. Genomic libraries were screened, and germline VH segments representing each of these new families were identified. The VH segments are closely linked and interspersed with members of different VH families. Each of these germline gene segments shared characteristic structural features: an upstream region that contained transcriptional regulatory elements, a leader sequence split by a short intron, an open reading frame encoding readily identified framework and complementarity determining regions, and a terminal recombination signal sequence consisting of a consensus heptamer, a 22-24 bp spacer with conserved 5'- and 3'-ends, and a consensus A-rich nonamer. Southern blot analyses estimate the number of members within these new families ranges from small (2-7 members in VH9, VH10, and VH12) to medium (9-13 members in VH8, VH11, and VH13). Thus, there are between 165 and 200 germline VH segments represented by these combined 13 families with present analyses indicating that perhaps one-half of these are pseudogenes. Phylogenetic comparisons indicate that members of these different catfish VH families cluster within Groups C and D of vertebrate VH genes. These analyses also indicate that Group D is represented by two different branches and both branches include VH families from different lineages of bony fish that diverged early in vertebrate phylogeny.

Amino Acid Sequence↗
PubMed1993

The primary structure of sturgeon prolactin: phylogenetic implication.

The complete amino acid sequence of prolactin (PRL) from a chondrostean species, the sturgeon (Acipenser gueldenstaedti), has been determined. Sturgeon PRL was isolated from the pituitary glands by gel filtration on a Sephadex G-25 column and high-performance liquid chromatography on a reverse-phase column following acid-acetone extraction. Sturgeon PRL was identified by immunoblot reactivity using antisera against salmon and ovine PRL. It consists of 204 amino acid residues, which is the largest among known PRLs, and contains three disulfide bonds corresponding to those of tetrapod PRLs. Sequence comparison with PRLs from other vertebrates revealed that sturgeon PRL has slightly higher sequence identities (35-46%) with teleost PRLs than with tetrapod PRLs (30-40%). These structural characteristics imply that an ancestor of the ray-finned fishes had PRL with three disulfide bonds and at some point after divergence of Chondrostei, the disulfide bond in the amino-terminus of PRL was lost.

Amino Acid Sequence↗