Duplicate Gene Expression Research Articles

Evolution of nuclearly encoded mitochondrial genes in Metazoa

All Metazoan nuclear genomes underwent a continuous process of both complete and partial genetic material gain and loss. The forces modulating these events are also subject to the strict interaction between nuclear and mitochondrial (mt) genome. In this context we investigate the evolution of nuclear genes encoding proteins which target the mitochondrion, with a particular attention to genes involved in oxidative phosphorylation (OXPHOS), one of the most ancient and conserved functions. To examine thoroughly the evolutionary strategies that preserve OXPHOS and coordinate the two cellular genomes, a comparative analysis has been carried out for 78 OXPHOS gene families in several Metazoa (insects, tunicates, fishes and mammals). We demonstrate that the duplication rate of OXPHOS genes increases passing from invertebrates to vertebrates consistently with the total increase in genome size, but all species are prone to negatively select OXPHOS duplicates compared to the general trend of nuclear gene families. These results are consistent with the ‘balance hypothesis’ and, at least in insects, the expression of duplicate genes is low and strongly testis-biased.

Rapid evolution of expression and regulatory divergences after yeast gene duplication.

Although gene duplication is widely believed to be the major source of genetic novelty, how the expression or regulatory network of duplicate genes evolves remains poorly understood. In this article, we propose an additive expression distance between duplicate genes, so that the evolutionary rate of expression divergence after gene duplication can be estimated through phylogenomic analysis. We have analyzed yeast genome sequences, microarrays, and transcriptional regulatory networks, showing a >10-fold increase in the initial rate for both expression and regulatory network evolution after gene duplication but only an approximately 20% rate increase in the early stage for protein sequences. Based on the estimated age distribution of yeast duplicate genes, we roughly estimate that the initial rate of expression divergence shortly after gene duplication is 2.9 x 10(-9) per year, whereas the baseline rate for very ancient gene duplication is 0.14 x 10(-9) per year. Relative expression rate tests suggest that the expression of duplicate genes tends to evolve asymmetrically, that is, the expression of one copy evolves rapidly, whereas the other one largely maintains the ancestral expression profile. Our study highlights the crucial role of early rapid evolution after gene/genome duplication for continuously increasing the complexity of the yeast regulatory network.

Differential expression of duplicated genes for brain-type fatty acid-binding proteins ( fabp7a and fabp7b) during early development of the CNS in zebrafish ( Danio rerio)

A gene for the zebrafish brain-type fatty acid-binding protein ( fabp7b) was identified and its structure defined. The zebrafish fabp7b gene spans 1479 bp and consists of four exons encoding 24, 58, 34 and 16 amino acids, respectively, which is identical to the structure of the fabp7a gene previously described. The complete fabp7b cDNA was isolated by 5′ and 3′ RACE and its nucleotide sequence determined. The deduced amino acid sequence of FABP7B encoded by the zebrafish fabp7b gene shares 82% identity with that of FABP7A encoded by the zebrafish fabp7a gene. A single transcription start site for the fabp7b gene was mapped by 5′ RNA ligase-mediated RACE. Phylogenetic analysis indicated that the duplication of the fabp7 genes occurred in the fish lineage after their divergence from mammals. The zebrafish fabp7b gene was assigned to linkage group 20 by radiation hybrid mapping. Reverse transcription-polymerase chain reaction detected fabp7b transcripts in the same adult tissues as fabp7a transcripts. In the brain, levels of fabp7b transcripts were lower than fabp7a transcripts. Whole-mount in situ hybridization showed that the zebrafish fabp7a transcripts were distributed in the early developing central nervous system. In addition to being expressed in the developing brain and retina, zebrafish fabp7b mRNA was also detected in the swim bladder and pharynx during the embryonic to larval transitory phase.

Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing.

Most eukaryotes have genomes that exhibit high levels of gene redundancy, much of which seems to have arisen from one or more cycles of genome doubling. Polyploidy has been particularly prominent during flowering plant evolution, yielding duplicated genes (homoeologs) whose expression may be retained or lost either as an immediate consequence of polyploidization or on an evolutionary timescale. Expression of 40 homoeologous gene pairs was assayed by cDNA-single-stranded conformation polymorphism in natural (1- to 2-million-yr-old) and synthetic tetraploid cotton (Gossypium) to determine whether homoeologous gene pairs are expressed at equal levels after polyploid formation. Silencing or unequal expression of one homoeolog was documented for 10 of 40 genes examined in ovules of Gossypium hirsutum. Assays of homoeolog expression in 10 organs revealed variable expression levels and silencing, depending on the gene and organ examined. Remarkably, silencing and biased expression of some gene pairs are reciprocal and developmentally regulated, with one homoeolog showing silencing in some organs and the other being silenced in other organs, suggesting rapid subfunctionalization. Duplicate gene expression was examined in additional natural polyploids to characterize the pace at which expression alteration evolves. Analysis of a synthetic tetraploid revealed homoeolog expression and silencing patterns that sometimes mirrored those of the natural tetraploid. Both long-term and immediate responses to polyploidization were implicated. Data suggest that some silencing events are epigenetically induced during the allopolyploidization process.

Characterization of duplicated zebrafish cyp19 genes.

The zebrafish has recently been developed as a good genetic model system. We report here the use of zebrafish to study the regulation of estrogen biosynthesis. The CYP19 gene encodes cytochrome P450 aromatase, which catalyzes the synthesis of estrogens. Two cyp19 genes, termed cyp19a and cyp19b, have been isolated from zebrafish. Sequence comparison shows that Cyp19a and Cyp19b belong to two separate Cyp19 subfamilies. The cyp19a gene is expressed in the ovary, whereas cyp19b is expressed in the brain. The cyp19a and cyp19b genes are located on zebrafish chromosomes LG 18 and 25, respectively. Our data indicate that these gene loci arose through an ancient chromosomal duplication event. The expression of duplicated genes in distinct tissues may have evolutionary significance.

Two Cyp19 (P450 Aromatase) Genes on Duplicated Zebrafish Chromosomes Are Expressed in Ovary or Brain

Cytochrome P450 aromatase (Cyp19) is an enzyme catalyzing the synthesis of estrogens, thereby controlling various physiological functions of estrogens. We isolated two cyp19 cDNAs, termed cyp19a and cyp19b, respectively, from zebrafish. These genes are located in linkage groups 18 and 25, respectively. Detailed gene mapping indicated that zebrafish linkage groups 18 and 25 may have arisen from the same ancestral chromosome by a chromosome duplication event. Cyp19a is expressed mainly in the follicular cells lining the vitellogenic oocytes in the ovary during vitellogenesis. Cyp19b is expressed abundantly in the brain, at the hypothalamus and ventral telencephalon, extending to the olfactory bulbs. The expression of duplicated cyp19 genes at two different tissues highlights the evolutionary significance of maintaining two active genes on duplicated zebrafish chromosomes for specific functions in the ovary and the brain.

Isozymes of the Isoetes riparia Complex, II. Ancestry and Relationships of Polyploids

Abstract Isoetes riparia is a complex tetraploid taxon of eastern North America that in its widest sense includes a diversity of morphotypes variously segregated, or included in a single polymorphic species. Although the diploid ancestry of I. riparia has been proposed as I. echinospora × engelmannii, it is uncertain whether this ancestry applies to all elements of the complex, here broadly defined to encompass three segregates of I. riparia and the recently described I. hyemalis (referred to informally as riparia, canadensis, saccharata and hyemalis). To help clarify relationships among these tetraploids, isozyme genotypes for 13 loci coding eight enzymes, were determined for 16 populations representing all four segregates. Duplicate gene expression, evidenced as fixed heterozygosity consistent with allopolyploidy, characterized the tetraploid genotypes of all taxa. Although exhibiting modest to no variation within populations, populations were highly differentiated, most showing a unique combination of ...

Levels and patterns of genetic variation in the endangered speciesAbronia macrocarpa(Nyctaginaceae)

Genetic variation was evaluated in the federally endangered species Abronia macrocarpa (large-fruited sand-verbena), an herbaceous perennial restricted to deep sandy soils and endemic to three counties of east-central Texas. Seven of the ten known populations were sampled and analyzed using starch gel electrophoresis of eight enzymes coded by 18 interpretable loci. Duplicate gene expression was observed for four loci, suggesting polyploid ancestry for the lineage that includes A. macrocarpa. Values for estimators of genetic polymorphism within populations (ranges: P = 38.9%-61.1%, A = 1.7-2.1, H = 0.122-0.279) exceeded average values for seed plants (P = 34.2%, A = 1.53, H = 0.113). Genotype proportions at most loci in most populations were in Hardy-Weinberg equilibrium, consistent with obligate outcrossing previously documented for this species; exceptions could be attributed to population substructure. Values of F(ST) tended to be high, ranging from 0.021 to 0.481 for individual loci (mean F(ST) = 0.272), indicating substantial divergence and limited gene flow among populations, despite their close geographic proximity. Pairwise values of Nei's genetic identity between populations ranged from 0.799 to 0.975 and tended to be influenced by geographic proximity of population pairs. Collectively, these data suggest a long history of isolation among populations that have not been subjected to bottlenecks. Isolation of A. macrocarpa populations apparently results from the disjunct occurrence of suitable habitat and perhaps has been accentuated by human disturbance.

Physical mapping of duplicated genomic regions of two chromosome ends in rice.

Two genomic regions duplicated in distal ends of the short arms of chromosomes 11 and 12 in rice (Oryza sativa L.) were characterized by YAC ordering with 46 genetic markers. Physical maps covering most of the duplicated regions were generated. Thirty-five markers, including 21 rice cDNA clones, showed the duplicated loci arrayed strictly in the same order along the two specific genomic regions. Regardless of their different genetic distances, the two duplicated segments may have a similar and minimum physical size with an expected length of about 2.5 Mb. However, differences of RFLP frequency for the duplicated DNA copies and recombination frequency for a given homoeologous area between the two regions were observed, indicating that these changes in genome organization occurred after the duplication. Our results establish a good model system for resolving the relationships between gene duplication, expression of duplicated genes, and the frequency of meiotic recombination in small chromosomal regions.

Expression of multiple DQB genes in Bos indicus cattle.

Polymorphism of expressed bovine major histocompatibility complex (MHC) class II DQB genes was investigated in a group of nine MHC-homozygous Kenya Boran cattle (Bos indicus). DQB second exon fragments were amplified by reverse transcription-polymerase chain reaction of total mononuclear cell RNA, cloned and sequenced. While a single DQB sequence was obtained from some animals, two DQB exon 2 sequences were found in others, implying expression of duplicated DQB genes. Two pairs of duplicated DQB genes were found in this group of homozygotes, and sequence analysis showed that both pairs contained distinct DQB alleles. One DQB duplication was observed in two related animals with the same MHC haplotype (F100 and F188), while the second was detected in three animals (F187, G166 and G277) that expressed the same class II DRB3 and DQB alleles but had different class I (BoLA-A) types, suggesting that this DR/DQ haplotype may be widespread in Boran cattle.

Pattern of nucleotide substitutions in growth hormone-prolactin gene family: a paradigm for evolution by gene duplication.

The growth hormone-prolactin gene family in mammals is an interesting example of evolution by gene duplication. Divergence among members of duplicated gene families and among species was examined by using reported gene sequences of growth hormone, prolactin and their receptors. Sequence divergence among species was found to show a general tendency in which a generation-time effect is pronounced for synonymous substitutions but not so for nonsynonymous substitutions. Divergence among duplicated genes is characterized by the relatively high rate of nonsynonymous substitutions, i.e., the rate is close to that of synonymous ones. In view of the stage- and tissue-specific expression of duplicated genes, some of the amino acid substitutions among duplicated genes is likely to be caused by positive Darwinian selection.

Duplicate Gene Expression for Isocitrate Dehydrogenase and 6-Phosphogluconate Dehydrogenase in diploid Species of Eleusine (Gramineae)

Duplicate Gene Expression for Isocitrate Dehydrogenase and 6-Phosphogluconate Dehydrogenase in diploid Species of Eleusine (Gramineae)

Duplicate Gene Expression and Allozyme Divergence Diagnostic for Catostomus tahoensis and the Endangered Chasmistes cujus in Pyramid Lake, Nevada

The allotetraploid catostomid fish, Catostomus tahoensis and the endangered Chasmistes cujus, from Pyramid Lake, Nevada, were examined electrophoretically for duplicate gene expression and allozyme variation. Both species resemble other advanced catostomids in the retention of relatively few ancestrally duplicated genes: 34% and 36%, respectively. The two species were diagnostically different for 20 genetic characters: number of genes for fructose-bisphosphate aldolase (Fba-A'), tissue expression of an NADP-dependent malate dehydrogenase, and allelic composition at 18 loci. No genetic evidence of hybridization was detected in a sample of 28 C. cujus suspected, on the basis of morphology, to be of hybrid origin.

Two anthranilate synthase genes in Arabidopsis: defense-related regulation of the tryptophan pathway.

Arabidopsis thaliana has two genes, ASA1 and ASA2, encoding the alpha subunit of anthranilate synthase, the enzyme catalyzing the first reaction in the tryptophan biosynthetic pathway. As a branchpoint enzyme in aromatic amino acid biosynthesis, anthranilate synthase has an important regulatory role. The sequences of the plant genes are homologous to their microbial counterparts. Both predicted proteins have putative chloroplast transit peptides at their amino termini and conserved amino acids involved in feedback inhibition by tryptophan. ASA1 and ASA2 cDNAs complement anthranilate synthase alpha subunit mutations in the yeast Saccharomyces cerevisiae and in Escherichia coli, confirming that both genes encode functional anthranilate synthase proteins. The distributions of ASA1 and ASA2 mRNAs in various parts of Arabidopsis plants are overlapping but nonidentical, and ASA1 mRNA is approximately 10 times more abundant in whole plants. Whereas ASA2 is expressed at a constitutive basal level, ASA1 is induced by wounding and bacterial pathogen infiltration, suggesting a novel role for ASA1 in the production of tryptophan pathway metabolites as part of an Arabidopsis defense response. Regulation of key steps in aromatic amino acid biosynthesis in Arabidopsis appears to involve differential expression of duplicated genes.

Malate dehydrogenase in subtropical fish belonging to the orders characiformes, siluriformes and perciformes I. Duplicate gene expression and polymorphism

1. 1. Electrophoretic analysis of the soluble malate dehydrogenase (sMDH) from 22 subtropical fish belonging to the orders Characiformes, Siluriformes and Perciformes, collected in 10 reservoirs of São Paulo State and in two lakes of Minas Gerais State, Brazil, indicates that at least two sMDH loci, MDH-A ∗ and MDH-B ∗, are active. In addition to this latter locus, in Hoplias malabaricus (Erythrinidae, Characiformes), a MDH-A 1,3 ∗ isoloci is proposed in order to explain the six-banded pattern detected in all the individuals screened. 2. 2. In attempting to explain the multiplicity of compounds detected in 87% of the Geophagus brasiliensis (Cichlidae, Perciformes) specimens analyzed, three hypotheses are proposed: the event of duplication in processing the presence of three loci with a null allele within the MDH-B ∗, and overdominance. 3. 3. In 87% of the species here studied, a bidirectionally divergent pattern of expression of the sMDH loci was observed, in which the least anodal isozyme A 2 predominated in liver, and the most anodal isozyme B 2 predominated in skeletal muscle. In two siluriform species, Pimelodela gracilis and Hypostomus regani, and in one perciform, Tilapia rendalli, a unidirectionally divergent pattern, in which the isozyme A 2 predominated in every tissue analyzed, was observed. 4. 4. Polymorphism in at least one of the sMDH loci was detected in 9% of the species studied here: Leporinus friderici (Characiformes) at the MDH-A ∗ and P. gracilis at both sMDH loci. In L. friderici and Pimelodus maculatus (Siluriformes), rare alleles at the MDH-B ∗ locus were detected. Polymorphism at the mitochondrial locus was detected in Tilapia rendalli.

Divergence of duplicate genes in the three sciaenid species (Perciformes) from the south coast of Uruguay

1. 1. The extent of divergence of duplicate gene expression was determined to enzyme and tissue, by Klebe's method, in three species from family Sciaenidae (Perciformes). 2. 2. In the multilocus isozyme systems studied (PGI, LDH, CK and s-MDH) non-divergent gene expression among all tissues is present in 28% of the set patterns, unidirectionally divergent in 22% and bidirectionally divergent in 50%. 3. 3. An analysis of the evolution of the expression of duplicate genes from primitive to advanced fishes, and an interrelation of the four enzymes in the metabolism are presented.

The pattern of inheritance in apple (Malus X domestica Borkh.): further results from leaf isozyme analysis

Eight progenies from controlled crosses and one self-progeny of apple were analysed by electrophoresis for six leaf enzymes. Based on a polyploid origin for this species, three hypotheses were tested: monogenie disomic, bigenic disomic and tetrasomic inheritance. Three enzymes exhibited monogenic inheritance; two exhibited bigenic disomic inheritance specified by two homoeologous genes; and one exhibited bigenic disomic inheritance due to two linked genes. In all cases tetrasomic inheritance was disproved. These results agreed with previous data obtained from pollen isozyme analysis. They indicated a probable allopolyploid origin of the apple genome and the loss of duplicated gene expression in some cases.

Adaptative features of enzymes from family sciaenidae—III. Studies on lactate dehydrogenase (LDH) of fishes from the south coast of Uruguay

1. 1. Electrophoretic analyses of lactate dehydrogenase isozyme patterns of three species of temperate fish belonging to family Sciaenidae (order Perciformes) indicates that at least three LDH loci— Ldh-A, Ldh-B and Ldh-C are active. 2. 2. The subunits encoded by these loci occurred at different levels in the different tissues and organs analyzed. 3. 3. The products of these loci show different response to changes in temperature. The results were obtained by electrophoretic analyses. 4. 4. Thermostability of skeletal muscle, heart and eye lactate dehydrogenase incubated at 60°C for different periods of time were examined. 5. 5. Relative activities of LDH isozymes were compared by Klebe's method to determine pattern of divergence of duplicated gene expression in the three species studied.

Adaptative features of enzymes from family sciaenidae (perciformes)—I. studies on soluble malate dehydrogenase ( s-MDH) and creatine kinase (CK) of fishes from the south coast of uruguay

1. 1. Electrophoretic analysis of the soluble malate dehydrogenase ( s-MDH) and creatine kinase (CK) isozyme patterns of three species of temperate fishes (Sciaenidae, Perciformes) indicates at least two loci for s-MDH, Mdh-A and Mdh-B, and four CK, Ck-A, Ck-B, Ck-C and Ck-D. 2. 2. The subunits encoded by these loci occurred at different levels in different tissues and organs analyzed. 3. 3. Through electrophoretic analysis the products of these loci showed different behaviour to changes in temperature. 4. 4. Relative activities of s-MDH and CK isozymes were compared by Klebe's (1975) method to determine pattern of divergence of duplicated gene expression in the three studied species.

Adaptative features of enzymes from family sciaenidae—II. Studies on phosphoglucose isomerase (PGI) of fishes from the south coast of uruguay

1. 1. The electrokinetic and thermostability properties of phosphoglucose isomerase (PGI) in three species of temperate fishes (Perciformes, Acanthopterygii)— Cynoscion striatus, Macrodon ancylodon and Micropogonias furnieri—have been analyzed in order to study the adaptative nature of protein heterogeneity found in ectotherms. 2. 2. Unlike most diploid fishes the PGI of these species seemed to be encoded by three PGI loci. 3. 3. The subunits encoded by these loci occured at different levels in the different tissues and organs analyzed. 4. 4. Genetic variants at two loci (Pgi-A and Pgi-B 2) were detected in Cynoscion striatus, and at one (Pgi-A) in Micropogonias furnieri. 5. 5. The product of these loci could be separated in three PGI regions based on their electrophoretic distribution and thermostability properties. 6. 6. The more anodal region (including isozymes and allozymes) was more thermolabile than the less anodal one, which is predominant in a single tissue skeletal muscle. 7. 7. Relative activities of PGI isozymes were compared by Klebe's method to determine pattern of divergence of duplicated gene expression in the three species studied.