Does negative auto-regulation increase gene duplicability?

Abstract:

BACKGROUND:A prerequisite for a duplication to spread through and persist in a given population is retaining expression of both gene copies. Yet changing a gene's dosage is frequently detrimental to fitness. Consequently, dosage-sensitive genes are less likely to duplicate. However, in cases where the level of gene product is controlled, via negative feedback, by its own abundance, an increase in gene copy number can in principle be decoupled from an increase in protein while both copies remain expressed. Using data from the transcriptional networks of E. coli and S. cerevisiae, we test the hypothesis that genes under negative auto-regulation show enhanced duplicability. RESULTS:Controlling for several known correlates of duplicability, we find no statistically significant support in either E. coli or S. cerevisiae that transcription factors under negative auto-regulation hold a duplicability advantage over transcription factors with no auto-regulation. CONCLUSION:Based on the analysis of transcriptional networks in E. coli and S. cerevisiae, there is no evidence that negative auto-regulation has contributed, on a genome-wide scale, to the variability in gene family sizes in these species.

journal_name

BMC Evol Biol

journal_title

BMC evolutionary biology

authors

Warnecke T,Wang GZ,Lercher MJ,Hurst LD

doi

10.1186/1471-2148-9-193

subject

Has Abstract

pub_date

2009-08-07 00:00:00

pages

193

issn

1471-2148

pii

1471-2148-9-193

journal_volume

9

pub_type

杂志文章
  • Oceanic dispersal barriers, adaptation and larval retention: an interdisciplinary assessment of potential factors maintaining a phylogeographic break between sister lineages of an African prawn.

    abstract:BACKGROUND:Genetic breaks separating regional lineages of marine organisms with potentially high broadcasting abilities are generally attributed either to dispersal barriers such as currents or upwelling, or to behavioural strategies promoting self-recruitment. We investigated whether such patterns could potentially al...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-8-341

    authors: Teske PR,Papadopoulos I,Newman BK,Dworschak PC,McQuaid CD,Barker NP

    更新日期:2008-12-24 00:00:00

  • A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks.

    abstract:BACKGROUND:Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila. RES...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-019-1472-6

    authors: Rosani U,Bai CM,Maso L,Shapiro M,Abbadi M,Domeneghetti S,Wang CM,Cendron L,MacCarthy T,Venier P

    更新日期:2019-07-23 00:00:00

  • Annotating long intergenic non-coding RNAs under artificial selection during chicken domestication.

    abstract:BACKGROUND:Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefor...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-017-1036-6

    authors: Wang YM,Xu HB,Wang MS,Otecko NO,Ye LQ,Wu DD,Zhang YP

    更新日期:2017-08-15 00:00:00

  • 3D shape analyses of extant primate and fossil hominin vertebrae support the ancestral shape hypothesis for intervertebral disc herniation.

    abstract:BACKGROUND:Recently we proposed an evolutionary explanation for a spinal pathology that afflicts many people, intervertebral disc herniation (Plomp et al. [2015] BMC Evolutionary Biology 15, 68). Using 2D data, we found that the bodies and pedicles of lower vertebrae of pathological humans were more similar in shape to...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-019-1550-9

    authors: Plomp KA,Dobney K,Weston DA,Strand Viðarsdóttir U,Collard M

    更新日期:2019-12-16 00:00:00

  • The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold.

    abstract:BACKGROUND:Bacterial populations are highly successful at colonizing new habitats and adapting to changing environmental conditions, partly due to their capacity to evolve novel virulence and metabolic pathways in response to stress conditions and to shuffle them by horizontal gene transfer (HGT). A common theme in the...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-273

    authors: Fernandez FJ,Garces F,López-Estepa M,Aguilar J,Baldomà L,Coll M,Badia J,Vega MC

    更新日期:2011-09-26 00:00:00

  • Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes.

    abstract:BACKGROUND:Developing lepidopteran microsatellite DNA markers can be problematical, as markers often exhibit multiple banding patterns and high frequencies of non-amplifying "null" alleles. Previous studies identified sequences flanking simple sequence repeat (SSR) units that are shared among many lepidopteran species ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-10-144

    authors: Tay WT,Behere GT,Batterham P,Heckel DG

    更新日期:2010-05-17 00:00:00

  • A glimpse on the pattern of rodent diversification: a phylogenetic approach.

    abstract:BACKGROUND:Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroev...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-12-88

    authors: Fabre PH,Hautier L,Dimitrov D,Douzery EJ

    更新日期:2012-06-14 00:00:00

  • Reproductive consequences of an extra long-term sperm storage organ.

    abstract:BACKGROUND:Sperm storage plays a key role in the reproductive success of many sexually-reproducing organisms, and the capacity of long-term sperm storage varies across species. While there are theoretical explanations for why such variation exists, to date there are no controlled empirical tests of the reproductive con...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-020-01704-6

    authors: Dhillon A,Chowdhury T,Morbey YE,Moehring AJ

    更新日期:2020-11-30 00:00:00

  • Fused eco29kIR- and M genes coding for a fully functional hybrid polypeptide as a model of molecular evolution of restriction-modification systems.

    abstract:BACKGROUND:The discovery of restriction endonucleases and modification DNA methyltransferases, key instruments of genetic engineering, opened a new era of molecular biology through development of the recombinant DNA technology. Today, the number of potential proteins assigned to type II restriction enzymes alone is bey...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-35

    authors: Mokrishcheva ML,Solonin AS,Nikitin DV

    更新日期:2011-02-03 00:00:00

  • Reconstructing the muscular ground pattern of phylactolaemate bryozoans: first data from gelatinous representatives.

    abstract:BACKGROUND:Phylactolaemata is commonly regarded the earliest branch within Bryozoa and thus the sister group to the other bryozoan taxa, Cyclostomata and Gymnolaemata. Therefore, the taxon is important for the reconstruction of the bryozoan morphological ground pattern. In this study the myoanatomy of Pectinatella magn...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-017-1068-y

    authors: Gawin N,Wanninger A,Schwaha T

    更新日期:2017-11-07 00:00:00

  • Phenotypic integration of brain size and head morphology in Lake Tanganyika Cichlids.

    abstract:BACKGROUND:Phenotypic integration among different anatomical parts of the head is a common phenomenon across vertebrates. Interestingly, despite centuries of research into the factors that contribute to the existing variation in brain size among vertebrates, little is known about the role of phenotypic integration in b...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-14-39

    authors: Tsuboi M,Gonzalez-Voyer A,Kolm N

    更新日期:2014-03-04 00:00:00

  • Interspecific competition between entomopathogenic nematodes (Steinernema) is modified by their bacterial symbionts (Xenorhabdus).

    abstract:BACKGROUND:Symbioses between invertebrates and prokaryotes are biological systems of particular interest in order to study the evolution of mutualism. The symbioses between the entomopathogenic nematodes Steinernema and their bacterial symbiont Xenorhabdus are very tractable model systems. Previous studies demonstrated...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-6-68

    authors: Sicard M,Hinsinger J,Le Brun N,Pages S,Boemare N,Moulia C

    更新日期:2006-09-05 00:00:00

  • The population genetics of wild chimpanzees in Cameroon and Nigeria suggests a positive role for selection in the evolution of chimpanzee subspecies.

    abstract:BACKGROUND:Chimpanzees (Pan troglodytes) can be divided into four subspecies. Substantial phylogenetic evidence suggests that these subspecies can be grouped into two distinct lineages: a western African group that includes P. t. verus and P. t. ellioti and a central/eastern African group that includes P. t. troglodyte...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-014-0276-y

    authors: Mitchell MW,Locatelli S,Ghobrial L,Pokempner AA,Sesink Clee PR,Abwe EE,Nicholas A,Nkembi L,Anthony NM,Morgan BJ,Fotso R,Peeters M,Hahn BH,Gonder MK

    更新日期:2015-01-21 00:00:00

  • Expansions and contractions in gene families of independently-evolved blood-feeding insects.

    abstract:BACKGROUND:The blood-feeding behavior evolved multiple times in Insecta lineages and it represents an excellent opportunity to study patterns of convergent molecular evolution regarding this habit. In insects the expansion of some gene families is linked with blood-feeding behavior, but a wide study comparing the evolu...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-020-01650-3

    authors: Freitas L,Nery MF

    更新日期:2020-07-17 00:00:00

  • New transitional fossil snakeflies from China illuminate the early evolution of Raphidioptera.

    abstract:BACKGROUND:Raphidioptera (snakeflies) is a holometabolous order of the superorder Neuropterida characterized by the narrowly elongate adult prothorax and the long female ovipositor. Mesozoic snakeflies were markedly more diverse than the modern ones are. However, the evolutionary history of Raphidioptera is largely une...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-14-84

    authors: Liu X,Ren D,Yang D

    更新日期:2014-04-18 00:00:00

  • The mitochondrial phylogeny of an ancient lineage of ray-finned fishes (Polypteridae) with implications for the evolution of body elongation, pelvic fin loss, and craniofacial morphology in Osteichthyes.

    abstract:BACKGROUND:The family Polypteridae, commonly known as "bichirs", is a lineage that diverged early in the evolutionary history of Actinopterygii (ray-finned fish), but has been the subject of far less evolutionary study than other members of that clade. Uncovering patterns of morphological change within Polypteridae pro...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-10-21

    authors: Suzuki D,Brandley MC,Tokita M

    更新日期:2010-01-25 00:00:00

  • Evolutionary study of duplications of the miRNA machinery in aphids associated with striking rate acceleration and changes in expression profiles.

    abstract:BACKGROUND:The sequencing of the genome of the pea aphid Acyrthosiphon pisum revealed an unusual expansion of the miRNA machinery, with two argonaute-1, two dicer-1 and four pasha gene copies. In this report, we have undertaken a deeper evolutionary analysis of the phylogenetic timing of these gene duplications and of ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-12-216

    authors: Ortiz-Rivas B,Jaubert-Possamai S,Tanguy S,Gauthier JP,Tagu D,Claude R

    更新日期:2012-11-12 00:00:00

  • Variation in cyanogenic compounds concentration within a Heliconius butterfly community: does mimicry explain everything?

    abstract:BACKGROUND:Aposematic species advertise their unpalatability using warning signals such as striking coloration. Given that predators need to sample aposematic prey to learn that they are unprofitable, prey with similar warning signals share the cost of predator learning. This reduction in predation risk drives evolutio...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-016-0843-5

    authors: Arias M,Meichanetzoglou A,Elias M,Rosser N,de-Silva DL,Nay B,Llaurens V

    更新日期:2016-12-15 00:00:00

  • Recombinational micro-evolution of functionally different metallothionein promoter alleles from Orchesella cincta.

    abstract:BACKGROUND:Metallothionein (mt) transcription is elevated in heavy metal tolerant field populations of Orchesella cincta (Collembola). This suggests that natural selection acts on transcriptional regulation of mt in springtails at sites where cadmium (Cd) levels in soil reach toxic values This study investigates the na...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-7-88

    authors: Janssens TK,Mariën J,Cenijn P,Legler J,van Straalen NM,Roelofs D

    更新日期:2007-06-11 00:00:00

  • Evolutionary analysis of the kinesin light chain genes in the yellow fever mosquito Aedes aegypti: gene duplication as a source for novel early zygotic genes.

    abstract:BACKGROUND:The maternal zygotic transition marks the time at which transcription from the zygotic genome is initiated and a subset of maternal RNAs are progressively degraded in the developing embryo. A number of early zygotic genes have been identified in Drosophila melanogaster and comparisons to sequenced mosquito g...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-10-206

    authors: Biedler JK,Tu Z

    更新日期:2010-07-08 00:00:00

  • Molecular evolution of Phox-related regulatory subunits for NADPH oxidase enzymes.

    abstract:BACKGROUND:The reactive oxygen-generating NADPH oxidases (Noxes) function in a variety of biological roles, and can be broadly classified into those that are regulated by subunit interactions and those that are regulated by calcium. The prototypical subunit-regulated Nox, Nox2, is the membrane-associated catalytic subu...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-7-178

    authors: Kawahara T,Lambeth JD

    更新日期:2007-09-27 00:00:00

  • A general scenario of Hox gene inventory variation among major sarcopterygian lineages.

    abstract:BACKGROUND:Hox genes are known to play a key role in shaping the body plan of metazoans. Evolutionary dynamics of these genes is therefore essential in explaining patterns of evolutionary diversity. Among extant sarcopterygians comprising both lobe-finned fishes and tetrapods, our knowledge of the Hox genes and cluster...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-25

    authors: Liang D,Wu R,Geng J,Wang C,Zhang P

    更新日期:2011-01-26 00:00:00

  • Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids.

    abstract:BACKGROUND:Rosids are a major clade in the angiosperms containing 13 orders and about one-third of angiosperm species. Recent molecular analyses recognized two major groups (i.e., fabids with seven orders and malvids with three orders). However, phylogenetic relationships within the two groups and among fabids, malvids...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-7-217

    authors: Zhu XY,Chase MW,Qiu YL,Kong HZ,Dilcher DL,Li JH,Chen ZD

    更新日期:2007-11-10 00:00:00

  • The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella.

    abstract:BACKGROUND:Publication of the first diatom genome, that of Thalassiosira pseudonana, established it as a model species for experimental and genomic studies of diatoms. Virtually every ensuing study has treated T. pseudonana as a marine diatom, with genomic and experimental data valued for their insights into the ecolog...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-125

    authors: Alverson AJ,Beszteri B,Julius ML,Theriot EC

    更新日期:2011-05-14 00:00:00

  • Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation.

    abstract:BACKGROUND:The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-019-1384-5

    authors: Li ZH,Ma X,Wang DY,Li YX,Wang CW,Jin XH

    更新日期:2019-02-26 00:00:00

  • Towards a comprehensive characterization of durum wheat landraces in Moroccan traditional agrosystems: analysing genetic diversity in the light of geography, farmers' taxonomy and tetraploid wheat domestication history.

    abstract:BACKGROUND:Crop diversity managed by smallholder farmers in traditional agrosystems is the outcome of historical and current processes interacting at various spatial scales, and influenced by factors such as farming practices and environmental pressures. Only recently have studies started to consider the complexity of ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-014-0264-2

    authors: Sahri A,Chentoufi L,Arbaoui M,Ardisson M,Belqadi L,Birouk A,Roumet P,Muller MH

    更新日期:2014-12-21 00:00:00

  • Ancient lineage, young troglobites: recent colonization of caves by Nesticella spiders.

    abstract:BACKGROUND:The evolution and origin of cave organisms is a recurring issue in evolutionary studies, but analyses are often hindered by the inaccessibility of caves, morphological convergence, and complex colonization processes. Here we investigated the evolutionary history of Nesticella cave spiders, which are mainly d...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-13-183

    authors: Zhang Y,Li S

    更新日期:2013-09-04 00:00:00

  • Comparative phylogeography of the plateau zokor (Eospalax baileyi) and its host-associated flea (Neopsylla paranoma) in the Qinghai-Tibet Plateau.

    abstract:BACKGROUND:Specific host-parasite systems often embody a particular co-distribution phenomenon, in which the parasite's phylogeographic pattern is dependent on its host. In practice, however, both congruent and incongruent phylogeographic patterns between the host and the parasite have been reported. Here, we compared ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-014-0180-5

    authors: Lin G,Zhao F,Chen H,Deng X,Su J,Zhang T

    更新日期:2014-08-17 00:00:00

  • Integration of molecules and new fossils supports a Triassic origin for Lepidosauria (lizards, snakes, and tuatara).

    abstract:BACKGROUND:Lepidosauria (lizards, snakes, tuatara) is a globally distributed and ecologically important group of over 9,000 reptile species. The earliest fossil records are currently restricted to the Late Triassic and often dated to 227 million years ago (Mya). As these early records include taxa that are relatively d...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-13-208

    authors: Jones ME,Anderson CL,Hipsley CA,Müller J,Evans SE,Schoch RR

    更新日期:2013-09-25 00:00:00

  • Should sex-ratio distorting parasites abandon horizontal transmission?

    abstract:BACKGROUND:Sex-ratio distorting parasites are of interest due to their effects upon host population dynamics and their potential to influence the evolution of host sex determination systems. In theory, the ability to distort host sex-ratios allows a parasite with efficient vertical (hereditary) transmission to dispense...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-370

    authors: Ironside JE,Smith JE,Hatcher MJ,Dunn AM

    更新日期:2011-12-21 00:00:00