scholarly journals Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution

Science ◽  
2013 ◽  
Vol 342 (6154) ◽  
pp. 104-108 ◽  
Author(s):  
Christopher R. Baker ◽  
Victor Hanson-Smith ◽  
Alexander D. Johnson
Keyword(s):  
Gene Duplication ◽  
Large Set ◽  
Gene Products ◽  
Duplicated Genes ◽  
Mads Box ◽  
Competitive Interference ◽  
Regulatory Complexity ◽  
Gene Regulatory ◽  
Molecular Complexity ◽  
Gene Duplicate

Most models of gene duplication assume that the ancestral functions of the preduplication gene are independent and can therefore be neatly partitioned between descendant paralogs. However, many gene products, such as transcriptional regulators, are components within cooperative assemblies; here, we show that a natural consequence of duplication and divergence of such proteins can be competitive interference between the paralogs. Our example is based on the duplication of the essential MADS-box transcriptional regulator Mcm1, which is found in all fungi and regulates a large set of genes. We show that a set of historical amino acid sequence substitutions minimized paralog interference in contemporary species and, in doing so, increased the molecular complexity of this gene regulatory network. We propose that paralog interference is a common constraint on gene duplicate evolution, and its resolution, which can generate additional regulatory complexity, is needed to stabilize duplicated genes in the genome.

scholarly journals The Relationship between AGAMOUS and Cytokinin Signaling in the Establishment of Carpeloid Features

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 827
Author(s):  
Andrea Gómez-Felipe ◽  
Daniel Kierzkowski ◽  
Stefan de Folter
Keyword(s):  
Regulatory Network ◽  
Dependent Manner ◽  
Mads Box ◽  
Type B ◽  
Cytokinin Signaling ◽  
Reproductive Structures ◽  
Carpel Development ◽  
Gene Regulatory ◽  
The Relationship ◽  
Gynoecium Development

Gynoecium development is dependent on gene regulation and hormonal pathway interactions. The phytohormones auxin and cytokinin are involved in many developmental programs, where cytokinin is normally important for cell division and meristem activity, while auxin induces cell differentiation and organ initiation in the shoot. The MADS-box transcription factor AGAMOUS (AG) is important for the development of the reproductive structures of the flower. Here, we focus on the relationship between AG and cytokinin in Arabidopsis thaliana, and use the weak ag-12 and the strong ag-1 allele. We found that cytokinin induces carpeloid features in an AG-dependent manner and the expression of the transcription factors CRC, SHP2, and SPT that are involved in carpel development. AG is important for gynoecium development, and contributes to regulating, or else directly regulates CRC, SHP2, and SPT. All four genes respond to either reduced or induced cytokinin signaling and have the potential to be regulated by cytokinin via the type-B ARR proteins. We generated a model of a gene regulatory network, where cytokinin signaling is mainly upstream and in parallel with AG activity.

Muller’s ratchet of the Y chromosome with gene conversion

Genetics ◽  
2021 ◽  
Author(s):  
Takahiro Sakamoto ◽  
Hideki Innan
Keyword(s):  
Gene Duplication ◽  
Gene Conversion ◽  
Y Chromosome ◽  
Conversion Rate ◽  
Single Copy ◽  
Duplicated Genes ◽  
Fitness Effect ◽  
Muller's Ratchet ◽  
Y Chromosomes ◽  
Muller’S Ratchet

Abstract Muller’s ratchet is a process in which deleterious mutations are fixed irreversibly in the absence of recombination. The degeneration of the Y chromosome, and the gradual loss of its genes, can be explained by Muller’s ratchet. However, most theories consider single-copy genes, and may not be applicable to Y chromosomes, which have a number of duplicated genes in many species, which are probably undergoing concerted evolution by gene conversion. We developed a model of Muller’s ratchet to explore the evolution of the Y chromosome. The model assumes a non-recombining chromosome with both single-copy and duplicated genes. We used analytical and simulation approaches to obtain the rate of gene loss in this model, with special attention to the role of gene conversion. Homogenization by gene conversion makes both duplicated copies either mutated or intact. The former promotes the ratchet, and the latter retards, and we ask which of these counteracting forces dominates under which conditions. We found that the effect of gene conversion is complex, and depends upon the fitness effect of gene duplication. When duplication has no effect on fitness, gene conversion accelerates the ratchet of both single-copy and duplicated genes. If duplication has an additive fitness effect, the ratchet of single-copy genes is accelerated by gene duplication, regardless of the gene conversion rate, whereas gene conversion slows the degeneration of duplicated genes. Our results suggest that the evolution of the Y chromosome involves several parameters, including the fitness effect of gene duplication by increasing dosage and gene conversion rate.

Patterns of gene duplication and functional diversification during the evolution of the AP1/SQUA subfamily of plant MADS-box genes

2007 ◽  
Vol 44 (1) ◽  
pp. 26-41 ◽  
Author(s):  
Hongyan Shan ◽  
Ning Zhang ◽  
Cuijing Liu ◽  
Guixia Xu ◽  
Jian Zhang ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Mads Box ◽  
Mads Box Genes ◽  
Functional Diversification

scholarly journals Intron retention enhances gene regulatory complexity in vertebrates

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Ulf Schmitz ◽  
Natalia Pinello ◽  
Fangzhi Jia ◽  
Sultan Alasmari ◽  
William Ritchie ◽  
...  
Keyword(s):  
Intron Retention ◽  
Regulatory Complexity ◽  
Gene Regulatory

scholarly journals Genes relocated between Drosophila chromosome arms evolve under relaxed selective constraints relative to non-relocated genes

2017 ◽  
Author(s):  
Margaret L. I. Hart ◽  
Ban L. Vu ◽  
Quinten Bolden ◽  
Keith T. Chen ◽  
Casey L. Oakes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Population Genetics ◽  
Comparative Genomics ◽  
Gene Duplication ◽  
Male Fertility ◽  
Chromosomal Location ◽  
Single Copy ◽  
Duplicated Genes ◽  
Selective Constraints ◽  
Functional Analyses

AbstractGene duplication creates a second copy of a gene either in tandem to the ancestral locus or dispersed to another chromosomal location. When the ancestral copy of a dispersed duplicate is lost from the genome, it creates the appearance that the gene was “relocated” from the ancestral locus to the derived location. Gene relocations may be as common as canonical dispersed duplications in which both the ancestral and derived copies are retained. Relocated genes appear to be under more selective constraints than the derived copies of canonical duplications, and they are possibly as conserved as single-copy non-relocated genes. To test this hypothesis, we combined comparative genomics, population genetics, gene expression, and functional analyses to assess the selection pressures acting on relocated, duplicated, and non-relocated single-copy genes in Drosophila genomes. We find that relocated genes evolve faster than single-copy non-relocated genes, and there is no evidence that this faster evolution is driven by positive selection. In addition, relocated genes are less essential for viability and male fertility than single-copy non-relocated genes, suggesting that relocated genes evolve fast because of relaxed selective constraints. However, relocated genes evolve slower than the derived copies of canonical dispersed duplicated genes. We therefore conclude that relocated genes are under more selective constraints than canonical duplicates, but are not as conserved as single-copy non-relocated genes.

scholarly journals Enhanced functional divergence of duplicate genes several million years after gene duplication in the Arabidopsis lineage

2016 ◽  
Author(s):  
Kousuke Hanada ◽  
Ayumi Tezuka ◽  
Masafumi Nozawa ◽  
Yutaka Suzuki ◽  
Sumio Sugano ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Synonymous Substitution ◽  
Duplicate Genes ◽  
Duplicated Genes ◽  
Highly Qualified ◽  
Duplication Events ◽  
Synonymous Substitution Rates

AbstractLineage-specifically duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selective pressures immediately after gene duplication is clear in the speciation process. Plants have substantially higher gene duplication rates than most other eukaryotes. Here, using Illumina short reads from Arabidopsis halleri, which has highly qualified plant genomes in close species (Brassica rapa, A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups among B. rapa, A. thaliana, A. lyrata and A. halleri. The frequency of duplication events in the Arabidopsis lineage was approximately 10 times higher than the frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss. Of the currently retained genes in A. halleri, 11–24% had undergone gene duplication in the Arabidopsis lineage. To examine the degree of selective pressure for duplicated genes, we calculated the ratios of nonsynonymous to synonymous substitution rates (KA/KS) in the A. halleri-lyrata and A. halleri lineages. Using a maximum-likelihood framework, we examined positive (KA/KS > 1) and purifying selection (KA/KS < 1) at a significant level (P < 0.01). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. More interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication at a higher proportion than immediately after gene duplication.

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

Genetics ◽  
1993 ◽  
Vol 134 (4) ◽  
pp. 1271-1276
Author(s):  
T Ohta
Keyword(s):  
Growth Hormone ◽  
Gene Duplication ◽  
Gene Family ◽  
High Rate ◽  
General Tendency ◽  
Duplicated Genes ◽  
Nucleotide Substitutions ◽  
Specific Expression ◽  
Nonsynonymous Substitutions ◽  
Prolactin Gene

Abstract 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.

scholarly journals Can ODE gene regulatory models neglect time lag or measurement scaling?

2020 ◽  
Vol 36 (13) ◽  
pp. 4058-4064
Author(s):  
Jie Hu ◽  
Huihui Qin ◽  
Xiaodan Fan
Keyword(s):  
Linear Regression ◽  
Regression Models ◽  
Time Course ◽  
Time Lag ◽  
Microarray Dataset ◽  
Gene Products ◽  
Linear Regression Models ◽  
Ode Models ◽  
Gene Regulatory ◽  
Regulatory Models

Abstract Motivation Many ordinary differential equation (ODE) models have been introduced to replace linear regression models for inferring gene regulatory relationships from time-course gene expression data. But, since the observed data are usually not direct measurements of the gene products or there is an unknown time lag in gene regulation, it is problematic to directly apply traditional ODE models or linear regression models. Results We introduce a lagged ODE model to infer lagged gene regulatory relationships from time-course measurements, which are modeled as linear transformation of the gene products. A time-course microarray dataset from a yeast cell-cycle study is used for simulation assessment of the methods and real data analysis. The results show that our method, by considering both time lag and measurement scaling, performs much better than other linear and ODE models. It indicates the necessity of explicitly modeling the time lag and measurement scaling in ODE gene regulatory models. Availability and implementation R code is available at https://www.sta.cuhk.edu.hk/xfan/share/lagODE.zip.

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