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PubMed1987

Diversification of the myofibrillar M-band in rat skeletal muscle during postnatal development.

The fine structure of the M-band in soleus (SOL) and extensor digitorum longus (EDL) muscles in newborn and four-week-old rats was studied using electron-microscopic techniques. In newborn rats, all myotubes and fibres in both muscles had an identical myofibrillar appearance. A five-line M-band pattern was seen in longitudinal sections and distinct M-bridges in cross-sections. The Z-discs were of medium width. On the other hand, in four-week-old rats, different muscle fibre types were observed on the basis of their myofibrillar pattern. In SOL two fibre types were distinguished in longitudinal sections. One had a four-line M-band pattern and very broad Z-discs, whereas the other type had five lines in the M-band and broad Z-discs. In EDL, three different myofibrillar patterns were observed. The M-bands were composed of three, four or five lines. Fibres had either thin, broad or medium Z-disc widths, respectively. In cross-sections of the SOL muscle one group of fibres showed indistinct M-bridges, whereas distinct M-bridges were seen in the other fibres and in all observed EDL muscle fibres. We conclude that initially there seems to be a single intrinsic program for M-band genesis; this program becomes modified upon the induction of functionally differentiated fibres.

Aging↗
PubMed1979

Evolutionary diversification of structure and function in the family of intracellular calcium-binding proteins.

The maximum parsimony method was used to reconstruct the genealogical history of the family of intracellular calcium-binding proteins represented by six major present-day lineages, three of which--calcium dependent modulator protein, heart and skeletal muscle troponin Cs, and alkali light chains of myosin--were found to share a closer kinship with one another than with the other lineages. Similarly, parvalbumins and regulatory light chains of myosin were depicted as more closely related, whereas the branch of intestinal calcium-binding protein proved to have the most distant separation. The computer-generated amino acid sequence for the common ancestor of these six lineages described a four domain protein in which each domain of approximately 40 amino acid residues had a mid-region. 12 residue segment that bound calcium and had properties most resembling those of the calcium dependent modulator protein. It could then be deduced that parvalbumins evolved by deletion of domain I, inactivation of calcium-binding properties in domain II, and acquisition of increased affinity for Ca++ and Mg++ in domains III and IV. Regulatory light chains of myosin lost the cation binding property from three domains, retaining it in I, whereas alkali light chains of myosin lost this ability from each of the four domains. In skeletal muscle troponin C all domains retained their calcium-binding activity; however, like parvalbumins, domains III and IV acquired high affinity properties. Cardiac troponin C lost its binding activity from domain I but otherwise resembled the skeletal muscle form. Finally, intestinal calcium-binding protein evolved by deletion of domains III and IV. Positive selection could be implicated in these evolutionary changes in that the rate of fixation of mutations substantially increased in the mid portions of those domains which were loosing calcium-binding activity. Likewise, when the cation binding sites were changing from low to high affinity, an accelerated rate of fixed mutations was observed. Once this new functional parameter was selected these regions showed a remarkable conservatism, as did those binding sites which were maintaining the lower affinity. Moreover even in sequence regions not directly involved in cation binding, the lineage of troponin C because very conservative over the past 300 million years, perhaps becuase of the necessity for maintaining specific interfaces in order for the molecule to interact with troponin I and T in a functional thin myofilament. A similar phenomenon was observed in domain II of the regulatory light chains of the myosin lineage suggesting a possible binding site with the heavy chain of myosin.

Amino Acid Sequence↗
PubMed1982

Accepted mutations in a gene family: evolutionary diversification of duplicated DNA.

We report and compare the DNA sequences of 14 silkmoth (Antheraea polyphemus) chorion genes, derived from either cDNA or chromosomal DNA clones. Seven of these genes are members of the A multigene family, and seven are members of the B family. Where available, the previously reported (Jones and Kafatos 1980) intronic and extragenic flanking DNA sequences are also considered. Closely related sequences are compared, revealing the types of spontaneous mutations that were fixed during paralogous evolution. Segmental mutations (i.e. mutations other than substitutions) are nearly always interpretable as small duplications or deletions, related to small direct repeats. Segmental mutations are strongly constrained in the coding regions, although they do occur. Nucleotide substitutions also appear to be under selective constraints: relatively few substitutions leading to amino acid replacements are accepted, silent substitutions leading to some codons (especially purine-terminated ones) are disfavored, and different compositional biases are maintained in different parts of the sequences. Other sequence differences can be interpreted as indicative of neutral drift, including most differences in non-coding regions and most T/C transitions in third-base positions. In the non-coding regions, which are thought to be only loosely constrained by selection, transitions are observed more frequently than might be expected: they account for 52% of all substitutions, and they appear to be favored two to threefold over transversions when allowance is made for the skewed base composition of these regions.

Base Sequence↗
PubMed1996

Molecular diversification of tandemly organized DNA sequences and heterochromatic chromosome regions in some Triticeae species.

The subtelomeric heterochromatin of rye (Secale cereale) chromosomes makes up 12-18% of the genome and consists largely of a small number of tandemly organized DNA sequence families. The genomic organization, chromosomal locations and the structural organization of monomer units of the major DNA sequences from these regions were investigated and compared in other Triticeae species from the genera Secale, Agropyron, Dasypyrum, Triticum and Hordeum. Southern hybridization and polymerase chain reaction analysis established that all studied species preserve the tandem type of sequence organization but the copy number is altered drastically between species. In the pSc200 family, a fraction of the tandem arrays is present with a head-to-head orientation of dimers in S. cereale and S. montanum. Members of the same family are more heterogeneous and present as head-to-head monomers in the Dasypyrum species and A. cristatum. In situ hybridization demonstrates different organization of the sequence families in the various species: pSc200 and pSc250 are concentrated in major blocks at the ends of most rye chromosome arms, whereas they are more dispersed and in smaller blocks in Dasypyrum and Agropyron, indicating that accumulation is not simply due to the sequence itself. In contrast to rye, D. villisum has large blocks of only pSc200 whereas D. breviaristatum shows greater amplification of pSc250. These data indicate that each repetitive family is an independent unit of evolution, and suggest that the two Dasypyrum species are not closely related. The data are discussed in terms of existing evolutionary models for repetitive DNA sequences. The contribution of random events, through molecular drive and selection, to the evolution of heterochromatic regions is considered.

Chromosomes↗
PubMed1996

Nucleotide sequence and presumed secondary structure of the 28S rRNA of pea aphid: implication for diversification of insect rRNA.

Determination of the entire nucleotide sequence of the aphid 28S ribosomal RNA gene (28S rDNA) revealed that it is 4,147 bp in length with a G + C content of 60.3%. Based on the nucleotide sequence, we constructed a presumed secondary-structure model of the aphid 28S rRNA which indicated that the aphid 28S rRNA is characterized by the length and high G + C content of its variable regions. The G + C content of the aphid's variable regions was much higher than that of the entire sequence of the 28S rRNA, which formed a striking contrast to those of Drosophila with the G + C content much lower than the entire 28S molecule. In this respect, the aphid 28S rRNA somewhat resembled those of vertebrates. This is the third report of a complete large-subunit rRNA sequence from an arthropod, and the first 28S rRNA sequence for a nondipterous insect.

Animals↗
PubMed1999

Dynamic diversification from a putative common ancestor of scorpion toxins affecting sodium, potassium, and chloride channels.

Scorpions have survived successfully over millions of years without detectable changes in their morphology. Instead, they have developed an efficient alomonal machinery and a stinging device supporting their needs for prey and defense. They produce a large variety of polypeptidic toxins that bind and modulate ion channel conductance in excitable tissues. The binding site, mode of action, and chemical properties of many toxins have been studied extensively, but little is known about their genomic organization and diversity. Genes representing each of the major classes of Buthidae scorpion toxins, namely, "long" toxins, affecting sodium channels (alpha, depressant, and excitatory), and "short" toxins, affecting potassium and chloride channels, were isolated from a single scorpion segment and analyzed. Each toxin type was found to be encoded by a gene family. Regardless of toxin length, 3-D structure, and site of action, all genes contain A+T-rich introns that split, at a conserved location, an amino acid codon of the signal sequence. The introns vary in length and sequence but display identical boundaries, agree with the GT/AG splice junctions, and contain T-runs downstream of a putative branch point, 5'-TAAT-3'. Despite little sequence similarity among all toxin classes, the conserved gene organization, intron features, and common cysteine-stabilized alpha-helical (CSH) core connecting an alpha-helix to a three-stranded beta-sheet suggest, that they all evolved from an ancestral common progenitor. Furthermore, the vast diversity found among genomic copies, cDNAs, and their protein products for each toxin suggests an extensive evolutionary process of the scorpion "pharmaceutical factory," whose success is due, most likely, to the inherent permissiveness of the toxin exterior to structural alterations.

Amino Acid Sequence↗
PubMed1999

DNA supercoiling and temperature adaptation: A clue to early diversification of life?

Cellular systems to control an appropriate DNA geometry for function probably evolved simultaneously with DNA genomes. Such systems are basically DNA topoisomerases and DNA-binding proteins. Therefore, their distribution in extant organisms may be a source of information on early evolution and the nature of the last common ancestor (cenancestor). Most living beings need the strand-opening potential of negative DNA supercoiling to allow transcription and other DNA-dependent processes. Mesophiles have global negatively supercoiled DNA, essentially due to gyrase (introducing negative supercoils) in bacteria and to DNA wrapping around histone cores in eukaryotes. Mesophilic archaea, halophilic methanogens, and halophiles might use a gyrase, whereas some methanogens might use histone wrapping. The existence of these two distinct mechanisms suggests that mesophily appeared at least twice in evolution. On the other hand, only one system which is based on reverse gyrase (introducing positive supercoils) appears to be required for hyperthermophilic life. Archaeal hyperthermophiles lacking gyrase have relaxed to positively supercoiled DNA, but hyperthermophilic bacteria of the genus Thermotoga, which have both gyrase and reverse gyrase, have negative supercoiling. This suggests that reverse gyrase is necessary at least locally, but whereas these hyperthermophilic bacteria favor general melting potential and stability at critical active regions, hyperthermophilic archaea favor general linking excess and local melting. In this context, the existence of a thermophilic (60-80 degrees C) ancestor endowed with only relaxing topoisomerases is hypothesized. Such temperatures allow a compromise between melting potential and stability, i.e., an appropriate DNA geometry for function. Subsequent duplication and functional specialization of existing DNA topoisomerases would then have facilitated adaptation to hyperthermophily and mesophily in archaea and bacteria, respectively. If reverse gyrase is an ancient character in hyperthermophilic bacteria, the cenancestor would have already been a hyperthermophile. Histone sequence homology and similarities of nucleosome structural dynamics suggest that eukaryotes inherited this system for DNA structural homeostasis from methanogenic euryarchaea. Some mesophilic archaea would have improved their adaptability to mesophily by importing gyrase from bacteria.

Archaea↗
PubMed1999

Evolutionary diversification of the mammalian defensins.

Defensins are cysteine-rich cationic peptides that function in antimicrobial defense in both invertebrates and vertebrates. Three main groups of animal defensins are known: insect defensins; mammalian alpha-defensins and vertebrate beta-defensins. It has been difficult to determine whether these molecules are homologous or have independently evolved similar features, but overall the evidence favors a distant relationship. The best evidence of this relationship is structural, particularly from their overall three-dimensional structure and from the spacing of half-cystine residues involved in intra-chain disulfide bonds. Some evidence favors a closer relationship between vertebrate beta-defensins and insect defensins than between the two groups of vertebrate defensins. Examination of nucleotide substitutions between recently duplicated mammalian defensin genes shows that the rate of nonsynonymous (amino-acid-altering) substitution exceeds that of synonymous substitution in the region of the gene encoding the mature defensin. This highly unusual pattern of nucleotide substitution is evidence that natural selection has acted to diversify defensins at the amino acid level. The resulting rapid evolution explains why it is difficult to reconstruct the evolutionary history of these molecules.

Amino Acid Sequence↗
PubMed2000

Origins and evolutionary diversification of the nuclear receptor superfamily.

Nuclear receptors (NRs), which include those for steroid and thyroid hormones as well as retinoids, are encoded by a large gene superfamily that has evolved to regulate nearly every facet of metazoan life, from development to basic metabolism. This article reviews the conservation in structure and function of distinct receptors across different species and attempts to draw conclusions as to the evolution of this gene superfamily. Although sequences related to NRs can be found in plants and yeast, gene sequence analyses suggest that the NR ancestor(s) first appeared in the early metazoans and subsequently diversified into the six receptor sub-families, which were already recognisable at the time of the Arthropoda-Chordata split over 700 million years ago. At the time when a primitive NR emerged, the basic components of the transcription regulatory machinery, which are conserved from yeast to vertebrates, were already in place and the ancestral NR must have evolved with the ability to communicate with them. The first such NRs likely acted as monomers and in a ligand-independent fashion. As members of the NR superfamily acquired the ability to hetero- and homodimerise, and to bind and be regulated by ligands, the functional complexity of the NR superfamily increased. This exponentially increasing complexity subsequently provided a potential driving force for evolution of higher organisms by supplying a sophisticated regulatory gene network that could control complex physiological processes during development and in adult organisms.

Amino Acid Sequence↗
PubMed2005

TRPC3: a versatile transducer molecule that serves integration and diversification of cellular signals.

Transient receptor potential (TRP) proteins have been recognized as sensors for a wide variety of external and internal signals involved in maintenance of cellular homeostasis and control of physiological functions. Evidence of a striking versatility in terms of signal integration and transduction has been reported for members of the canonical (or classical) TRP subfamily (TRPCs). TRPC species are cation channel subunits and emerge as multifunctional signal transduction molecules that are able to function as components of divergent signalplexes. Results obtained in heterologous expression systems suggest TRPC3 as a paradigm of multifunctional signal transduction by a cation channel protein. TRPC3 serves cellular Ca(2+) signaling by multiple mechanisms and may control a variety of distinct physiological functions. In this review, we summarize current knowledge on the properties and possible signaling partners of TRPC3, and discuss the role of TRPC3 channel proteins in cellular signaling networks.

Animals↗
PubMed2003

The PRAT purine synthesis gene duplication in Drosophila melanogaster and Drosophila virilis is associated with a retrotransposition event and diversification of expression patterns.

The Drosophila melanogaster Prat gene encodes amidophosphoribosyltransferase (PRAT; EC 2.4.2.14), which performs the first step in de novo purine nucleotide synthesis. Prat mutations have a recessive lethal phenotype that is found for other genes encoding enzymes in this pathway. The D. melanogaster genome project has revealed a second gene, CG10078 or Prat2, encoding a protein with 76% amino acid sequence identity with Prat. The two genes map to different arms of chromosome 3 and have different intron/exon organizations, as we confirmed by cDNA sequence analysis of Prat2. With the goal to determine the functional significance of this gene duplication, we isolated and sequenced two PRAT-encoding genes from Drosophila virilis. We find that the two D. virilis genes are orthologous to the two D. melanogaster genes in terms of intron/exon organization, amino acid coding sequence, and 5' noncoding sequence. The absence of introns in both DmelPrat and DvirPrat genes suggests that Prat originated from a retrotransposition of Prat2 and that the gene duplication has been preserved in the two species since their divergence approximately 40 million years ago. Analysis of mRNA expression in development shows that maternal expression, detected in adult ovaries and embryos prior to the onset of zygotic transcription, is present for Prat but not Prat2 in both species. Taken together, these findings support the notion that two PRAT-encoding genes have evolved distinct functions in both Drosophila species.

Amidophosphoribosyltransferase↗
PubMed2003

Phylogenetic divergence of fish and mammalian metallothionein: relationships with structural diversification and organismal temperature.

Metallothioneins (MTs) are nonenzymatic low molecular weight proteins, that play an important role in the homeostasis and detoxification of heavy metals in a large variety of organisms. These proteins are endowed with striking features, including an unusual amino acid composition characterized by the presence of 20 cysteines out of a total of 60 residues and absence of secondary structure elements. It is generally accepted that MTs underwent few modifications during evolution because of these structural and functional constraints. Such a conclusion is founded on the studies carried out mostly on MTs of mammalian origin. For such a reason, we have decided to compare the MTs of homeothermic and poikilothermic organisms, such as mammals and fish, with the specific aim to put in relation phylogenetic divergence and structural/functional adaptation to temperature. We have included in our analysis also Antarctic Notothenioids, a fish group characterized by genetic isolation and cold-adaptation to a particular harsh environment. We have determined the average hydropathic index of ancestral MT sequences and used them to infer the temperatures of the environment housing the hypothetical ancestor organisms. Finally, we have derived phylogenetic relationships of MT molecules from the pairwise comparison of their three-dimensional structures.

Adaptation, Physiological↗
PubMed2004

Diversification of ftsZ during early land plant evolution.

The plastid division proteins FtsZ are encoded by a small nuclear gene family in land plants. Although it has been shown for some of the gene products that they are imported into plastids and function in plastid division, the evolution and function of this gene family and their products remain to be unraveled. Here we present two new ftsZ genes from the moss Physcomitrella patens and compare the genomic structure of members of the two plant ftsZ gene families. Comparison of sequence features and phylogenetic analyses confirm the presence of two clusters of paralogues in land plants and demonstrate that these genes were duplicated before the divergence of mosses, ferns and seed plants.

Amino Acid Sequence↗
PubMed2005

Phage associated bacteriocins reveal a novel mechanism for bacteriocin diversification in Klebsiella.

Ninety-six isolates of Klebsiella pneumoniae and K. oxytoca were recovered from wild mammals in Australia. 14.6% of these bacteria produce killing phenotypes that suggest the production of bacteriocin toxins. Cloning and sequencing of the gene clusters encoding two of these killing phenotypes revealed two instances of a bacteriocin associated with a bacteriophage gene, the first such genetic organization described. The newly identified klebicin C gene cluster was discovered in both K. pneumoniae and K. oxytoca. The newly identified klebicin D gene cluster was detected in K. oxytoca. Protein sequence comparisons and phylogenetic inference suggest that klebicin C is most closely related to the rRNase group of colicins (such as colicin E4), while klebicin D is most closely related to the tRNase group of colicins (such as colicin D). The klebicin C and D gene clusters have similar genetic and regulatory organizations. In both cases, an operon structure is inferred consisting of a phage-associated open reading frame and klebicin activity and associated immunity genes. This novel bacteriophage/bacteriocin organization may provide a novel mechanism for the generation of bacteriocin diversity in Klebsiella.

Bacteriocins↗
PubMed2006

Loss of introns along the evolutionary diversification pathway of snake venom disintegrins evidenced by sequence analysis of genomic DNA from Macrovipera lebetina transmediterranea and Echis ocellatus.

Analysis of cDNAs from Macrovipera lebetina transmediterranea (Mlt) and Echis ocellatus (Eo) venom gland libraries encoding disintegrins argued strongly for a common ancestry of the messengers of short disintegrins and those for precursors of dimeric disintegrin chains. We now report the sequence analysis of disintegrin-coding genes from these two vipers. Genomic DNAs for dimeric disintegrin subunits Ml_G1 and Ml_G2 (Mlt) and Eo_D3 (Eo) contain single 1-kb introns exhibiting the 5'-GTAAG (donor)/3'-AG (acceptor) consensus intron splicing signature. On the other hand, the short RTS-disintegrins Ml_G3 (Mlt) and Eo_RTS (Eo) and the short RGD-disintegrin ocellatusin (Eo) are transcribed from intronless genomic DNA sequences, indicating that the evolutionary pathway leading to the emergence of short disintegrins involved the removal of all intronic sequences. The insertion position of the intron within Ml_G1, Ml_G2, and Eo_D3 is conserved in the genes for vertebrate ADAM (A disintegrin and metalloproteinase) protein disintegrin-like domains and within the gene for the medium-size snake disintegrins halystatins 2 and 3. However, a comparative analysis of currently available disintegrin(-like) genes outlines the view that a minimization of both the gene organization and the protein structure underlies the evolution of the snake venom disintegrin family.

Amino Acid Sequence↗
PubMed2000

Reconstructing the diversification of alpha-esterases: comparing the gene clusters of Drosophila buzzatii and D. melanogaster.

A cluster composed of 10 active alpha-esterase genes and a pseudogene is distributed over 60 kb in the Drosophila melanogaster genome. This paper describes the corresponding cluster in Drosophila buzzatii, whose lineage diverged from that of D. melanogaster when the subgenera Drosophila and Sophophora diverged about 50 Mya. With three exceptions we find that the composition of the cluster is conserved in the two lineages. The location of alpha E1 in D. melanogaster differs from that of its nearest relative in D. buzzatii, and alpha E4 has duplicated independently in the two lineages. The nature of these differences indicates that a mechanism exists whereby copies of genes can be placed in opposite orientation and nonadjacent positions within a gene cluster, although this does not seem to be a feature of earlier events in the cluster's evolution. The rates of amino acid change are not significantly different between orthologs, but the rates differ sevenfold among paralogs, indicating that very different selective forces are acting on the genes of the cluster. Mapping of sequence differences onto a model of the tertiary structure of the enzymes indicates that motifs contributing to substrate binding and catalysis have changed radically in the alphaE4s and suggest that this subgroup of alpha-esterases may be evolving into a substantially different functional niche.

Animals↗
PubMed2001

Diversification of the microtubule system in the early stage of eukaryote evolution: elongation factor 1 alpha and alpha-tubulin protein phylogeny of termite symbiotic oxymonad and hypermastigote protists.

The symbiotic protists of the lower termite have been regarded as a model of early-branched eukaryotes because of their simple cellular systems and morphological features. However, cultivation of these symbiotic protists is very difficult. For this reason, these interesting protists have not been well characterized in terms of their molecular biology. In research on these organisms which have not yet been cultivated, we developed a method for retrieving specific genes from a small number of cells, through micromanipulation without axenic cultivation, and we obtained EF-1 alpha and alpha-tubulin genes from members of the Hypermastigida--the parabasalid protist Trichonympha agilis and the oxymonad protists Pyrsonympha grandis and Dinenympha exilis--from the termite Reticulitermes speratus gut community. Results of phylogenetic analysis of the amino acid sequences of both proteins, EF-1 alpha and alpha-tubulin, indicate that the hypermastigid, parabasalid, and oxymonad protists do not share a close common ancestor. In addition, although the EF-1 alpha phylogeny indicates that these two groups of protists branched at an early stage of eukaryotic evolution, the alpha-tubulin phylogeny indicates that these protists can be assigned to two diversified clades. As shown in a recent investigation of alpha-tubulin phylogeny, eukaryotic organisms can be divided into three classes: an animal--parabasalids clade, a plant--protists clade, and the diplomonads. In this study, we show that parabasalids, including hypermastigids, can be classified as belonging to the animal--parabasalids clade and the early-branching eukaryote oxymonads can be classified as belonging to the plant--protists clade. Our findings suggest that these protists have a cellular microtubule system that has diverged considerably, and it seems that such divergence of the microtubule system occurred in the earliest stage of eukaryotic evolution.

Animals↗