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PubMed1992

Unification of the ferritin family of proteins.

Ferritin is the iron-storage protein of eukaryotic organisms. The nucleotide sequence encoding Azotobacter vinelandii bacterioferritin, a hemoprotein, was determined. The deduced amino acid sequence reveals a high degree of identity with Escherichia coli bacterioferritin and a striking similarity to eukaryotic ferritins. Moreover, derivation of a global alignment shows that virtually all key residues specifying the unique structural motifs of eukaryotic ferritin are conserved or conservatively substituted in the A. vinelandii sequence. The alignment suggests specific methionine residues as heme-binding ligands in bacterioferritins. The overall sequence similarity with conservation of key structural residues implies that all ferritins form a unified family of proteins. The results implicate ferritins as proteins potentially common to all aerobic organisms and as such useful in taxonomic classification, evolutionary analysis, and environmental monitoring.

Amino Acid Sequence↗
PubMed1990

Evolution in bacterial plasmids and levels of selection.

Gene flow between different reproductive units such as bacterial plasmids and chromosomes presents unusual problems for evolutionary analysis. Far more than in eukaryotes, reproductive advantages at several levels of selection--genes, transposons, plasmids, cells, and clones--must be considered simultaneously to understand plasmid evolution. No level consistently prevails in conflict situations, and some reproductive units carry genes that restrain their own reproduction or survival, apparently to enhance the reproduction or survival of the higher-level reproductive units that carry them. Despite gene flow between plasmids and chromosomes, genes for certain functions show strong tendencies to occur on plasmids while others consistently occur on chromosomes. Functions generally associated with plasmids are diverse, but all are useful only in locally restricted contexts; it is argued that the selective consequences of the greater horizontal (within generation) transmission of plasmids are responsible for this pattern. The tendency for prokaryote transposons, which are also horizontally mobile, to carry genes similar to those commonly on plasmids supports this argument. The apparent trends in eukaryote plasmids and transposons to lack these same characters also accords with predictions of the local adaptation hypothesis, because genes on these genetic units are generally no more horizontally mobile than chromosomal genes. There are theoretical reasons to expect that plasmid genes tend to evolve more rapidly than chromosomal genes. "The selfish interests of genes have manifestly produced 'vehicles' in the forms of organelles, cells, individuals and yet higher units. If evolution is to predict as well as describe, then selfish interests must be understood in the framework of the constraints and opportunities generated by these 'vehicles'" (Buss, 1987, p. 182).

Bacteria↗
PubMed1979

An ethological view of human adolescence.

In modern times the essential "normality" of adolescence has been acknowledged. With its pan-cultural and functional perspective, ethology is in a position to elaborate a description of normal human adolescence. Ethologists attempt to elucidate four interrelated aspects of a given behavior: its survival function, evolution, development, and elicitation by internal and external factors. The basic research strategy is two-fold: to identify biologically based, or evolved, behaviors (chiefly by controlling for the effects of experience and seeing if a core of evolved behavior remains); and to discover their functions by isolating the necessary and sufficient ecological conditions for their evolution. Applying this evolutionary analysis to human adolescence, we find that two developments seem to be basic: reproductive maturation and gaining independence from parents. The remainder of the article is an interpretation of various behavioral, morphological, and cultural data in accordance with these two developmental functions. Puberty seems to be timed so as to promote these functions most effectively. Pubertal changes parallel somatic growth and are delayed by poor nutrition, disease, and psychological stress--patterns consistent with functional considerations. The influence of natural selection on the sequencing of pubertal events is also emphasized. The role of pubertal hormones in altering behavior as well as morphology is illustrated. The adolescent gains independence from his parents by means of maturation and sex differentiation. Males become specialized for vigorous exertion, and females for work near the settlement--although considerable overlap in morphological and behavioral tendencies exists between the sexes. Various examples of sex differentiation demonstrates how morphological, behavioral, and cultural factors complement each other. Adolescent initiation rites help channel boys and girls into appropriate adult roles, teach respect for one's culture, and favor the fittest individuals. Hopi rites of passage are described as an example. Reproductive maturation likewise involves adaptive morphological and behavioral changes that are reinforced by cultural mores. Males rely on intimidation more than females, in order to dominate other males and attract females; contrariwise, females employ an endearment strategy more than males do. Many sex differences in human reproductive behavior can be explained with reference to man's parental behavior pattern. These include the male's greater aggressiveness, the preponderance of polygyny over polyandry, and differences in the antecedents of jealousy. Lastly, the need for an ethological understanding of adolescence is underscored as promising to offer a useful perspective on the problems of U.S. youth.

Adolescent↗
PubMed2025

The landscape of structural variation in pediatric cancer.

Structural variants (SVs) account for over 60% of the driver variants in pediatric cancer, and in many cases act as the cancer initiating event. To study SVs from a pan-cancer perspective, we analyzed 1,616 pediatric cancer genomes in 16 major cancer types of hematological malignancies (n = 908), brain tumors (n = 183), and solid tumors (n = 525) and compared their profiles to those of 2,203 adult cancers. The SV burden varied ~100-fold across pediatric cancer types and demonstrated an 8- to 16-fold reduction compared to adult brain and solid tumors but was comparable in pediatric versus adult hematological malignancies. Recurrent SV hotspots occurred uniquely in pediatric acute lymphoblastic leukemias (ALLs) in proximity to RAG-mediated recombination signal sequences (RSS) and disrupted multiple immune-related loci as well as 69 genes, which often involved cryptic RSS sites. By contrast, such hotspots affected only immune-related loci but not driver genes in adult lymphoid cancers. Eight SV signatures extracted from the cohort had varying distributions across cancer types, with clustered translocations reflecting templated insertions in osteosarcoma, and medium-sized deletions (10 kb to 1 Mb) enriched in cancers with RAG-mediated deletions. Intra-patient evolutionary analysis in 13 patients with multiple spatiotemporally distinct samples revealed that RAG-mediated recombination in leukemia and complex rearrangements in solid tumors occurred both early in disease initiation and continuously during later diversification, contributing to clonal heterogeneity. Finally, we found that both driver genes and fragile sites were the two genomic regions most frequently disrupted by SVs. The unique and diverse SV landscapes that emerged from this comprehensive analysis expand the scope of RSS-mediated mutagenesis in pediatric ALL and will be a valuable resource for guiding future functional studies and the design of clinical genomic testing in pediatric cancer.

Journal Article↗
PubMed2025

Comparative Genomics of Sex-Determination-Related Genes Reveals Shared Evolutionary Patterns Between Bivalves and Mammals, but Not Fruit Flies.

The molecular basis of sex determination (SD), while being extensively studied in model organisms, remains poorly understood in many animal groups. Bivalves, a diverse class of molluscs with a variety of reproductive modes, represent an ideal yet challenging clade for investigating SD and the evolution of sexual systems. However, the absence of a comprehensive framework has limited progress in this field, particularly regarding the study of sex-determination-related genes (SRGs). In this study, we performed a genome-wide sequence evolutionary analysis of the Dmrt, Sox and Fox gene families in more than 40 bivalve species. For the first time, we provide an extensive and phylogenetically aware dataset of these SRGs, and we find support for the hypothesis that Dmrt-1L and Sox-H may act as primary sex-determining genes by showing their high levels of sequence diversity within the bivalve genomic context. To validate our findings, we studied the same gene families in two well-characterised systems, mammals and fruit flies (genus Drosophila). In the former, we found that the male sex-determining gene Sry exhibits a pattern of amino acid sequence diversity similar to that of Dmrt-1L and Sox-H in bivalves, consistent with its role as master SD regulator. In contrast, no such pattern was observed among genes of the fruit fly SD cascade, which is controlled by a chromosomic mechanism. Overall, our findings highlight similarities in the sequence evolution of some mammal and bivalve SRGs, possibly driven by a comparable architecture of SD cascades. This work underscores once again the importance of employing a comparative approach when investigating understudied and non-model systems.

Animals↗
PubMed1992

A second gene for the African green monkey poliovirus receptor that has no putative N-glycosylation site in the functional N-terminal immunoglobulin-like domain.

Using cDNA of the human poliovirus receptor (PVR) as a probe, two types of cDNA clones of the monkey homologs were isolated from a cDNA library prepared from an African green monkey kidney cell line. Either type of cDNA clone rendered mouse L cells permissive for poliovirus infection. Homologies of the amino acid sequences deduced from these cDNA sequences with that of human PVR were 90.2 and 86.4%, respectively. These two monkey PVRs were found to be encoded in two different loci of the genome. Evolutionary analysis suggested that duplication of the PVR gene in the monkey genome had occurred after the species differentiation between humans and monkeys. The NH2-terminal immunoglobulin-like domain, domain 1, of the second monkey PVR, which lacks a putative N-glycosylation site, mediated poliovirus infection. In addition, a human PVR mutant without N-glycosylation sites in domain 1 also promoted viral infection. These results suggest that domain 1 of the monkey receptor also harbors the binding site for poliovirus and that sugar moieties possibly attached to this domain of human PVR are dispensable for the virus-receptor interaction.

Amino Acid Sequence↗
PubMed1989

The genomics of long tandem arrays of satellite DNA in the human genome.

At least 10% of DNA in the human genome consists of long arrays of repeated sequences, arranged in tandem head-to-tail arrays in a number of discrete, highly localized chromosomal regions. Different families of these so-called "satellite DNA" sequences have been defined, organized in diverged subsets on different chromosomes. The molecular, cytogenetic, and evolutionary analysis of the hierarchical organization of such sequences in the human and other complex genomes encompasses a variety of approaches, including chromosomal mapping, in situ hybridization, genetic linkage analysis, long-range restriction mapping, and DNA sequencing. Investigation of the organization of satellite arrays constitutes a necessary first step towards eventual elucidation of the origin, evolution, and maintenance of these sequences and their contribution to the structure and behavior of human chromosomes.

Chromosome Mapping↗
PubMed2026

Identification of a novel HIV-1 circulating recombinant form (CRF209_cpx) and its descendant unique recombinant form (URF) CRF209_cpx/B among MSM in Guangdong, southern China.

BACKGROUND: The epidemic of human immunodeficiency virus type 1 (HIV-1) continues to pose a significant global health challenge, with increasing genetic diversity. The co-circulation of multiple subtypes among the local population facilitates the emergence of unique or circulating recombinant forms (URFs or CRFs). In China, the predominant strains include CRF07_BC, CRF01_AE, CRF55_01B, and subtype B. This study characterizes a novel CRF209_cpx and its descendant recombinant CRF209_cpx/B among men who have sex with men (MSM) in Guangdong, southern China. METHODS: Individuals infected with URFs with similar genetic characteristics were recruited during routine surveillance of pretreatment drug resistance. Near full-length genomes (NFLGs) were amplified with two overlapping fragments using a serial dilution nested PCR approach after reverse transcription. We used SimPlot and IQ-TREE softwares to conduct recombination analyses and phylogenetic inferences. Time-scaled maximum clade credibility (MCC) phylogenetic trees were reconstructed using BEAST software to estimate evolutionary origins. Genotypic drug resistance mutations were interpreted via the Stanford HIV Database, and coreceptor usage was predicted using geno2pheno coreceptor 2.5 and the HIVcoPRED tool. RESULTS: Four NFLG sequences were obtained and identified as a novel CRF209_cpx, generated by recombination among CRF01_AE, CRF07_BC and subtype B. Phylogenetic analyses revealed that all the parental segments clustered with lineages prevalent among MSM in China. Bayesian evolutionary analysis estimated that the most recent common ancestor (tMRCA) of CRF209_cpx to have evolved between 2011 and 2013. The fifth strain was identified as a URF recombined from nascent CRF209_cpx and B. No transmitted drug resistance mutation was detected in these five sequences. The four CRF209_cpx sequences primarily utilized the CXCR4 coreceptor, while the URF exhibited R5/X4 dual tropism. CONCLUSIONS: The emergence of the complex CRF209_cpx and novel URF of CRF209_cpx/B highlights the active HIV-1 epidemic within the MSM population in Guangdong, underscoring the necessity for enhanced molecular surveillance and precise public health intervention in this key population.

HIV-1↗
PubMed1992

The Myb DNA-binding domain is highly conserved in Dictyostelium discoideum.

The c-myb proto-oncogene encodes a protein that is highly conserved among birds and mammals. The amino-terminal domain of c-Myb contains three imperfect tandem repeats of approximately 50 amino acids each. This domain is required for DNA binding and has also been conserved to varying degrees in invertebrates, plants and yeast. Given that myb-related genes appear to control cellular differentiation in a variety of eucaryotic systems, the presence of a myb gene in the cellular slime mold Dictyostelium discoideum might provide a tractable system for studying the role of myb in differentiation. Degenerate oligonucleotide primers encoding regions that are highly conserved in the vertebrate and Drosophila Myb DNA-binding domains were used to amplify a related domain from Dictyostelium genomic DNA, which was then used to isolate a genomic clone. The putative DNA-binding domain of Dictyostelium Myb is as closely related to vertebrate c-Myb as is Drosophila Myb (65% identity), whereas the known Myb-related proteins of plants and yeast are more distantly related. The conserved domain of Dictyostelium Myb is capable of binding to the same DNA sequence as the vertebrate and Drosophila Myb proteins. The remainder of the deduced amino acid sequence of Dictyostelium Myb shows no homology to the divergent domains of the known animal, plant and yeast Myb-related proteins. Evolutionary analysis implies that the duplications that generated the repeats of the Myb DNA-binding domain began prior to the divergence of animals, plants, cellular slime molds and yeast.

Amino Acid Sequence↗
PubMed1990

Limitations of the evolutionary parsimony method of phylogenetic analysis.

Lake's evolutionary parsimony (EP) method of constructing a phylogenetic tree is primarily applied to four DNA sequences. In this method, three quantities--X, Y, and Z--that correspond to three possible unrooted trees are computed, and an invariance property of these quantities is used for choosing the best tree. However, Lake's method depends on a number of unrealistic assumptions. We therefore examined the theoretical basis of his method and reached the following conclusions: (1) When the rates of two transversional changes from a nucleotide are unequal, his invariance property breaks down. (2) Even if the rates of two transversional changes are equal, the invariance property requires some additional conditions. (3) When Kimura's two-parameter model of nucleotide substitution applies and the rate of nucleotide substitution varies greatly with branch, the EP method is generally better than the standard maximum-parsimony (MP) method in recovering the correct tree but is inferior to the neighbor-joining (NJ) and a few other distance matrix methods. (4) When the rate of nucleotide substitution is the same or nearly the same for all branches, the EP method is inferior to the MP method even if the proportion of transitional changes is high. (5) When Lake's assumptions fail, his chi2 test may identify an erroneous tree as the correct tree. This happens because the test is not for comparing different trees. (6) As long as a proper distance measure is used, the NJ method is better than the EP and MP methods whether there is a transition/transversion bias or whether there is variation in substitution rate among different nucleotide sites.

Base Sequence↗
PubMed1989

Kinetochore size variation in mammalian chromosomes: an image analysis study with evolutionary implications.

The kinetochore, a proteinaceous plate that is the site for attachment of spindle microtubules to the metaphase chromosome, can be visualized using anti-kinetochore indirect immunofluorescence. We have used computer-assisted image analysis to measure the variation of kinetochore surface areas, as reflected by immunofluorescence areas, in cell lines derived from rat kangaroo, Chinese hamster and common rat, to determine if our size estimates correlate well with those obtained using measurements from electron micrographs. In addition, we used male and female human fibroblast cell lines, as well as a transformed human female cell line as well as a transformed human female cell line (HeLa), to examine kinetochore size variation among cells, between sexes, and between cell lines. We found that our system gave reproducible estimates of kinetochore size, and that these sizes correlated very well (r = 0.95) with the electron micrograph measurements. In examining variation within humans, we observed measurable differences between cell lines. Despite this difference, all the human lines had size distributions that were leptokurtotic and positively skewed. The fact that very few chromosomes exhibited areas smaller than the mode gives support to the idea that mammalian chromosomes may require a specific, minimum amount of kinetochore material in order to maintain stable attachment to the mitotic spindle. On the other hand, the positive skewness seems to indicate that larger kinetochores, possibly the result of events such as Robertsonian fusions, are fully functional. The retention of this plasticity may allow the chromosomes to maintain an evolutionary adaptability that might otherwise be lost.

Animals↗
PubMed1991

The rat vitamin D binding protein (Gc-globulin) gene. Structural analysis, functional and evolutionary correlations.

The complete rat vitamin D binding protein (DBP) gene has been cloned and characterized. Genomic mapping suggests that there is only one copy of this gene in the haploid genome. The gene spans 35 kilobase pairs and contains 13 exons. All exons, exon/intron borders, and 2196 base pairs of 5'-flanking region have been sequenced. The transcription cap site, determined by primer extension analysis, is 62 base pairs upstream from the start of translation and predicts that an unusual TGTAAA motif may serve as a surrogate TATA. The promoter region contains about 50% nucleotide sequence similarity to the corresponding region of the partially characterized human DBP gene and is uniquely interrupted by a repetitive element. Although lacking in overall sequence similarity to the albumin (ALB) and alpha-fetoprotein (AFP) genes, the 5'-flanking region of the DBP gene contains a number of conserved segments which may correspond to critical proximal promoter elements in this gene family. The location of the introns in the coding region of the DBP gene is highly conserved when compared with the ALB and AFP genes. Detailed comparison of exon size and content confirms the previous prediction that the smaller size of the DBP protein results from loss of internal exons 12 and 13 from the DBP progenitor gene during its evolutionary divergence from ALB and AFP.

Amino Acid Sequence↗
PubMed1990

Cloning and structural analysis of a gene encoding a mouse mastocytoma proteoglycan core protein; analysis of its evolutionary relation to three cross hybridizing regions in the mouse genome.

Serglycin (SGC) is a Ser-Gly-repeat-containing protein, used as a proteoglycan core protein in the parietal yolk sac and in mast cells, where glycosaminoglycan side chains are attached to the serine residues of the repeat region. In this article, the structure of the gene SGC encoding mouse SGC is reported. The gene is divided into three exons, which are all contained within a region of approximately 13 kb. Nucleotide (nt) sequence analysis was carried out on a region of 1.2 kb upstream from the first exon. The region containing the two promoters (active in parietal yolk sac and in mast cells, respectively) was analyzed for the presence of recognition sites for known DNA-binding proteins. A number of sequences closely related to known recognition sites were found in both promoters, and one consensus octamer-binding site could be identified in the putative yolk-sac promoter. Multiple regions in the mouse genome hybridizing with DNA fragments covering the Ser-Gly repeat region have previously been described, and it has been suggested that these loci may represent other proteoglycan core proteins. Analysis of nt sequence was carried out on three out of the more than 15 of these regions present in the mouse genome. However, none of the clones analyzed was found to have any open reading frame in the region of cross-hybridization which possibly could code for a SGC protein. Instead, one of the clones was found to contain an exon encoding a highly basic protein, unrelated to SGC. Hence, no evidence was found for a multigene family of Ser-Gly-repeat-containing proteoglycan-encoding genes.

Aggrecans↗
PubMed2025

Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis.

Caspases are evolutionarily conserved proteins essential for driving cell death in development and host defense. Caspase-8, a key member of the caspase family, is implicated in nonlytic apoptosis, as well as lytic forms of cell death. Recently, caspase-8 has been identified as an integral component of PANoptosomes, multiprotein complexes formed in response to innate immune sensor activation. Several innate immune sensors can nucleate caspase-8-containing PANoptosome complexes to drive inflammatory lytic cell death, PANoptosis. However, how the evolutionarily conserved and diverse functions of caspase-8 drive PANoptosis remains unclear. To address this, we performed evolutionary, sequence, structural, and functional analyses to decode caspase-8's complex-forming abilities and its interaction with the PANoptosome adaptor ASC. Our study distinguished distinct subgroups within the death domain superfamily based on their evolutionary and functional relationships, identified homotypic traits among subfamily members, and captured key events in caspase evolution. We also identified critical residues defining the heterotypic interaction between caspase-8's death effector domain and ASC's pyrin domain, validated through cross-species analyses, dynamic simulations, and in vitro experiments. Overall, our study elucidated recent evolutionary adaptations of caspase-8 that allowed it to interact with ASC, improving our understanding of critical molecular associations in PANoptosome complex formation and the underlying PANoptotic responses in host defense and inflammation. These findings have implications for understanding mammalian immune responses and developing new therapeutic strategies for inflammatory diseases.

Caspase 8↗
PubMed1991

[Quantitative analysis of the teleost brain: evolutionary and adaptive characteristics of encephalization. III. Multivariate analysis of the cephalic index].

A multivariate analysis of 9 brain indices from 83 teleost species showed a marked opposition between the non-olfactory telencephalon (and diencephalon) and the medulla oblongata (phylogenetic characters) and between the olfactory bulbs and the optic tectum (adaptive characters). Results of three different classifying algorithms allowed determination of 6 stable groupings and 9 intermediate ones, some with systematic importance and some purely adaptive. For this reason brain organization criteria must be used with precaution for systematic purposes. Nevertheless, the position of Brotula multibarbata showed that this fish is an evolved acanthopterygian.

Adaptation, Physiological↗
PubMed1986

Evolutionary origin of autoreactive determinants (autogens).

The question addressed in this report focuses on the autoantigenicity of self antigens, principally cytochrome c and lysozyme. Of interest is whether the immune system produces autoantibodies to its host proteins reacting randomly with all potential antigen sites or is autoreactively selective for certain determinants. Based on experimental evidence from autoantibodies against cytochromes c, Jemmerson and Margoliash [Jemmerson, R. & Margoliash, E. (1979) Nature (London) 282, 468-471] have described a striking correlation between autoreactive sequence regions and evolutionary instability. While their analysis of evolutionary variation was based on simple sequence variability plots, we present here a refined approach that takes into account the distinction between evolutionary substitutions that induce a change in the protein surface from those that do not (surface-neutral substitutions). A quantitative aspect of surface variation (surface consensus) is included in the algorithm that produces a ranked order for autoantigenic determinants. The final plot, called surface variability, indicates sequence regions having a preference for autoimmune reaction. We propose the term "autogen" to designate such protein determinants.

Amino Acid Sequence↗
PubMed1990

Analysis of expression and evolutionary relationships of phosphoenolpyruvate carboxylase genes in Flaveria trinervia (C4) and F. pringlei (C3).

Phosphoenolpyruvate carboxylase (PEPCase) was shown to be encoded by a multigene family in various Flaveria species analysed. Several clones were isolated from genomic libraries of F. pringlei (C3 species) and F. trinervia (C4 species) and classified into four distinct groups according to their hybridization behaviour to a full-length cDNA clone encoding the PEPCase C4 isozyme of F. trinervia. A detailed cross-hybridization analysis demonstrated that the closest relative of most of the PEPCase genes isolated from F. trinervia and F. pringlei was not found in the same but in the other species. Northern analysis, using stringent conditions, allowed discrimination of class-specific PEPCase transcripts and revealed characteristic organ-specific expression patterns.

Biological Evolution↗