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PubMed1975

Gene duplication as a mechanism of genetic adaptation in Saccharomyces cerevisiae.

It has been shown that specific mutations of the gene that codes for the general acid monophophatase (Aphtase) of S. cerevisiae can increase the affinity of this enzyme for beta-glycerophosphate (BGP) and thereby provide this organism with the capacity to exploit extremely low concentrations of this organic phosphate (Francis and Hansche 1973). In this report two additional avenues are demonstrated to be available to this organism for increasing its capacity to exploit low concentrations of organic phosphates. One avenue is through mutations that increase the amount of Aphtase that associates with the cell wall, where it catalizes the hydrolysis of exogenous organic phosphates. The other avenue is through duplication of the gene that codes for Aphtase, doubling the amount of Aphtase synthesized.--The spontaneous duplication of the structural gene of Aphtase and the incorporation of the duplicate into this experimental population as a means of exploiting low concentrations of exogenous organic phosphates provides direct support for the first step of the mechanism through which new metabolic functions are postulated to evolve.

Acid Phosphatase↗
PubMed1978

Gene duplication in Saccharomyces cerevisiae.

Five independent duplications of the acid-phosphatase (aphtase) structural gene (acp1) were recovered from chemostat populations of S. cerevisiae that were subject to selection for in vivo hyper-aphtase activity. Two of the duplications arose spontaneously. Three of them were induced by UV. All five of the duplication events involved the transpositioning of the aphtase structural gene, acp1, and all known genes distal to acp1 on the right arm of chromosome II, to the terminus of an arm of other unknown chromosomes. One of the five duplicated regions of the right arm of chromosome II was found to be transmitted mitotically and meiotically with very high fidelity. The other four duplicated regions of the right arm of chromosome II were found to be unstable, being lost at a rate of about 2% per mitosis. However, selection for increased fidelity of mitotic transmission was effective in one of these strains. No tandem duplications of the aphtase structural gene were found.

Acid Phosphatase↗
PubMed2026

Adaptive deletion of functional duplicate genes in Drosophila.

Gene deletion is traditionally viewed as a nonadaptive mechanism that eliminates functional redundancy, yet emerging evidence indicates that it disproportionately affects tissue-specific duplicates with unique functions. Here, we test whether gene deletion preferentially removes weakly constrained, degenerating duplicates or instead eliminates functionally active duplicates through an adaptive process. To identify the evolutionary and functional factors that determine which duplicates are lost, we systematically analyzed 100 gene deletion events in Drosophila by integrating sequence, expression, interaction, and structural data. We uncovered a strong bias toward the loss of younger child copies among functionally unique duplicates, whereas no such bias was observed for redundant duplicates. Contrary to expectations under relaxed constraint, deleted functionally unique genes evolve more slowly, show higher expression, engage in more protein-protein interactions, and do not exhibit elevated structural divergence or intrinsic disorder relative to redundant duplicates. When compared with single-copy genes, deleted functionally unique genes display similar evolutionary rates, slightly lower expression, greater network connectivity, comparable structural divergence, and lower intrinsic disorder. These patterns suggest that deletion frequently affects functionally active rather than degenerate genes. Collectively, our results support the hypothesis that gene deletion in Drosophila can represent an adaptive process acting on transiently functional duplicates, potentially driven by either genome streamlining or context-dependent deleterious effects.

evolution↗
PubMed1979

Polymorphism and loss of duplicate gene expression: a theoretical study with application of tetraploid fish.

We studied the fixation of null alleles at independent duplicate loci, assuming that wild-type active alleles mutate irreversibly to nonfunctional null alleles and that the population is finite and panmictic. Solving the two-dimensional Kolmogorov backward equation numerically, we obtained the rate at which one of the active genes is lost and the amount of heterozygosity at specified times. Previously harmful genes, including recessive lethals, can be fixed at one of the duplicate loci, which would not happen with a single locus. Examination of data from several fish families showed that the rate of fixation of null alleles is too slow and the amount of heterozygosity too small to be compatible with complete recessivity at all loci. Our conclusion differs in this regard from that of Bailey et al. [Bailey, G.S., Poulter, R. T. M. & Stockwell, P. A. (1978) Proc. Natl. Acad. Sci. USA 75, 5575--5579]. They also reported that the time taken for 50% of the loci to be fixed for null alleles is approximately 15N + v-3/4, in which N and v are the effective population sizgote is lethal. We found that the fixation rate depends not only on N, but also on Nv.

Alleles↗
PubMed1979

Duplicate gene expression in tetraploid fishes of the tribe Moxostomatini (Cypriniformes, Catostomidae).

1. Karyotypically tetraploid fishes of the catostomid tribe Moxostomatini were electrophoretically examined to ascertain in the genetic control of 14 enzyme systems (21 loci in dipoid Cypriniformes). 2. The Moxostomatini have become functionally diploid at 50% or more of their loci since the original polyploidization event in the catosomid line. 3. The subgenera Megapharynx and Moxostoma s.s. (genus Moxostoma) are recognized as comprising a single lineage on the basis of synapomorphic diploidization at the G-3-pdh-A locus. 4. Thoburnia s.l. is allied with the genus Hypentelium on the basis of synapomorphic diploidization at the M-Aat-A locus supporting separate generic status for Thorburnia s.l.

Animals↗
PubMed2026

Genome-wide characterization of the bZIP gene family in Rattus norvegicus and expression profiling analysis during brain development.

BACKGROUND: The brown rat (Rattus norvegicus) serves as a cornerstone model organism in biomedical research, particularly for understanding physiological homeostasis and stress responses. The basic leucine zipper (bZIP) transcription factor family is a pivotal regulatory network involved in growth, organogenesis, and neurodevelopment. Despite its importance, a systematic characterization of the bZIP gene family in rats has remained elusive. RESULTS: In this study, we performed a genome-wide identification of 61 RnbZIP genes, which were categorized into 10 distinct subfamilies based on phylogenetic relationships and chromosomal localization. Structural analysis revealed conserved motif arrangements within subfamilies, while collinearity analysis identified significant gene duplication events-predominantly tandem and segmental duplications-that have driven the evolutionary expansion of the RnbZIP family. Quantitative analysis showed that members within the same subfamily shared 45%-92% sequence similarity (calculated using the BLOSUM62 scoring matrix), and all duplicated gene pairs underwent strong purifying selection (Ka/Ks&#x2009;<&#x2009;1). Comparative genomics across seven rodent species further underscored the evolutionary conservation and divergence of these factors. Expression profiling across diverse organs and brain developmental stages indicated that RnbZIP genes exhibit high tissue specificity. Notably, 10 candidate genes, including RnbZIP01, RnbZIP02, and RnbZIP08, demonstrated dynamic expression patterns during brain maturation, suggesting their essential roles in neurodevelopmental processes. CONCLUSIONS: Our findings provide a comprehensive structural and evolutionary framework for the RnbZIP gene family, highlighting their potential regulatory functions in rat organogenesis and brain development. This study establishes a valuable resource for further functional characterization of specific bZIP members in mammalian neurological systems.

Animals↗
PubMed1976

Multiple forms of cyclohexanone oxygenase from Nocardia globerula CL1.

The cyclohexanone 1,2-monooxygenase of Nocardia globerula CL1 exists as two electrophoretically distinct forms. These are present in crude cell extracts and are not artifacts of enzyme purification or electrophoresis. They have been separated in mg amounts by preparative polyacrylamide gel electrophoresis and shown to have essentially identical kinetic, spectral and physical characteristics. They do differ in pH-activity profile and temperature stability. Whether or not they are conformational isoenzymes or arise by gene duplication and divergent evolution has not been established. Cyclohexanone oxygenase constitutes 8% of the soluble protein of induced cells. This high level would correlate well with the presence of duplicate genes. It is proposed that the presence of a large amount of cyclohexanone oxygenase may confer an ecological advantage on the organism.

Drug Stability↗
PubMed2025

doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.

SUMMARY: Gene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface. AVAILABILITY AND IMPLEMENTATION: doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/.

Software↗
PubMed2025

Gene and Genome Duplication in Spiders.

Gene and genome duplications are widely observed across various organisms, including plants, yeasts, and animals. Numerous studies link gene duplications to the emergence of novel phenotypes, supporting the hypothesis that duplication events are advantageous for adaptive evolution. Whole-genome duplications (WGD) are especially prevalent in plants and have also occurred ancestrally in vertebrates. However, large-scale duplication events in other animal groups remain understudied, partly due to limited genomic resources. Arthropods, particularly insects, represent one of the most diverse animal clades in terms of both species and phenotypic diversity. With increasing availability of chromosome-level genomes, large-scale duplications appear to be rare in insects but are more frequent in chelicerates (e.g. spiders, scorpions, and horseshoe crabs). This makes chelicerates an intriguing group for comparing the mechanisms, fates, and evolutionary impacts of large-scale duplications with those seen in plants and vertebrates. In this review, we synthesize and discuss current research on WGD in spiders and discuss different scenarios for genes following gene duplication events (conservation, nonfunctionalization, subfunctionalization, specialization, drift, neofunctionalization) in the context of experimental studies. We hypothesize if there might be common trajectories after duplication and how these could be tested.

Animals↗
PubMed1975

Duplication of the haemoglobin alpha-gene.

Gene duplication is one of the basic processes underlying evolutionary changes. The gamma-chains of human foetal haemoglobin is coded by multiple structural genes. The delta-chains of Hb A2 can be regarded as a duplication of the beta-locus. We have presented the first evidence for the presence of two major alpha-chain loci in man. The alpha-gene appears to have duplicated recently, since apart of the single point mutations characterizing Hb J-Buda and Hb G-Pest, the two alpha-gene products seem to be identical. Sensitive immunochemical measurement techniques may reveal structural differences which might escape detection by chemical methods based on differences in charge and/or chromatographic behaviour. Anti-alpha-chain sera recognizing the single amino acid substitution in alphaJ-Buda could be raised in rabbits. The anti-alpha-chain sera were found to be more powerful tools for detecting differences in the primary structure of the chain than the immune sera raised against the whole tetramer. None of the immune sera could reliably differentiate Hb G-Pest from Hb A1. The relative strength of complement fixation of the alpha-chains from haemoglobin A1 F and A2 was compared by hybridizing these human haemoglobins with caninehaemoglobin and measuring the quantitative complement fixation of the different hybrids with anti-Hb A1 and anti-alphaA1 rabbit immune sera. No antigenic difference among the alpha-chains from haemoglobins A1, A2 and F could be detected by this method either with anti-A1 or with anti-alphaA1 sera. These results do not exclude the possibility of conformational differences between the alpha-chains in native Hb A and Hb F. The antigenic activity of the alpha-chains of Hb A from normal subjects (alphaA1) and of the alpha-chains of Hb A from a double heterozygote for alphaJ-Buda and alphaG-Pest (alphaA1) were compared by the complement fixation technique. Definite differences could be detected in the relative strength of complement fixation by alphaA1 and alphaA1 with anti-alphaA1 serum. Final decision as to whether alpha-chain duplication is a universal phenomenon or whether it is restricted to only a part of mankind cannot be drawn until the presence of a silent alpha-thalassaemia gene is not excluded in some debated cases by reliable chemical methods. Measurement of alpha-globin genes in Hb H disease with cDNA enriched in alpha-globin sequences provided direct evidence that a non-thalassaemic subject has to have at least four alpha-globin genes per diploid cell.

Chromosome Mapping↗
PubMed1978

Direct demonstration of duplicate tuf genes in enteric bacteria.

Radioactive tuf mRNA was used to detect the tuf gene in bacterial DNA that had been digested by various restriction endonucleases. Both the K-12 and the B strains of Escherichia coli contain two tuf genes, but no more than two. Salmonella typhimurium also contains duplicate tuf genes.

Coliphages↗