Molecular Evolution of the Mammalian Alpha 2B Adrenergic Receptor

Madsen, Ole; Willemsen, Diederik; Ursing, Björn M.; Árnason, Úlfur; Jong, Wilfried W. de

doi:10.1093/oxfordjournals.molbev.a004040

Cited by 25 publications

(14 citation statements)

References 64 publications

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“…The maximum likelihood tree topology was inferred using the stepwise addition option of the BASEML program in the PAML package and is shown in Figure 5. Our tree closely matched the tree published by Madsen et al, (2002). A complete list of the species analyzed, their GenBank accession numbers, and the aligned sequences are available from http://rannala.org.…”

Section: Co Lusupporting

confidence: 67%

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Inferring Complex DNA Substitution Processes on Phylogenies Using Uniformization and Data Augmentation

Mateiu

Rannala

2006

Systematic Biology

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A new method is developed for calculating sequence substitution probabilities using Markov chain Monte Carlo (MCMC) methods. The basic strategy is to use uniformization to transform the original continuous time Markov process into a Poisson substitution process and a discrete Markov chain of state transitions. An efficient MCMC algorithm for evaluating substitution probabilities by this approach using a continuous gamma distribution to model site-specific rates is outlined. The method is applied to the problem of inferring branch lengths and site-specific rates from nucleotide sequences under a general time-reversible (GTR) model and a computer program BYPASSR is developed. Simulations are used to examine the performance of the new program relative to an existing program BASEML that uses a discrete approximation for the gamma distributed prior on site-specific rates. It is found that BASEML and BYPASSR are in close agreement when inferring branch lengths, regardless of the number of rate categories used, but that BASEML tends to underestimate high site-specific substitution rates, and to overestimate intermediate rates, when fewer than 50 rate categories are used. Rate estimates obtained using BASEML agree more closely with those of BYPASSR as the number of rate categories increases. Analyses of the posterior distributions of site-specific rates from BYPASSR suggest that a large number of taxa are needed to obtain precise estimates of site-specific rates, especially when rates are very high or very low. The method is applied to analyze 45 sequences of the alpha 2B adrenergic receptor gene (A2AB) from a sample of eutherian taxa. In general, the pattern expected for regions under negative selection is observed with third codon positions having the highest inferred rates, followed by first codon positions and with second codon positions having the lowest inferred rates. Several sites show exceptionally high substitution rates at second codon positions that may represent the effects of positive selection.

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Section: Co Lusupporting

confidence: 67%

“…The A2AB gene contains no introns, and studies examining sequence variation among mammals have revealed that different protein domains vary greatly in their degree of conservation, suggesting that variable selection pressures operate across the gene (Madsen et al, 2002).…”

Section: Co Lumentioning

confidence: 99%

Inferring Complex DNA Substitution Processes on Phylogenies Using Uniformization and Data Augmentation

Mateiu

Rannala

2006

Systematic Biology

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“…These results were congruent with those from the morphological and mt genome analyses Springer et al, 2004;Wildman et al, 2006). Madsen et al (2002) attempted to evaluate the utility of Alpha 2B adrenergic receptor gene in the Laurasiatheria phylogeny, which showed the tree as (Perissodactyla, ((Eulipotyphla, Cetartiodactyla), (Chiroptera, Carnivora, Pholidota))) ( Figure 1I, Table 1). Surprisingly, Perissodactyla was placed as the basal and Eulipotyphla was the sister-group of Cetartiodactyla.…”

Section: Phylogenetic Estimate From Nuclear Genessupporting

confidence: 68%

Summary of Laurasiatheria (Mammalia) Phylogeny

Zhang²,

Yu³

2013

Zoological Research

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Laurasiatheria is one of the richest and most diverse superorders of placental mammals. Because this group had a rapid evolutionary radiation, the phylogenetic relationships among the six orders of Laurasiatheria remain a subject of heated debate and several issues related to its phylogeny remain open. Reconstructing the true phylogenetic relationships of Laurasiatheria is a significant case study in evolutionary biology due to the diversity of this suborder and such research will have significant implications for biodiversity conservation. We review the higher-level (inter-ordinal) phylogenies of Laurasiatheria based on previous cytogenetic, morphological and molecular data, and discuss the controversies of its phylogenetic relationship. This review aims to outline future researches on Laurasiatheria phylogeny and adaptive evolution.

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“…Moreover, the enriched glutamate stretch could provide an acidic milieu essential for phosphorylation of the 80K-H PKC substrate. Evolutionary and functional studies showed that variation in length and acidity of similar domains are related to the degree of phosphorylation needed for receptor desensitization (38,39).…”

Section: K-h As a Ca 2ϩ -Dependent Regulator Of Trpv5mentioning

confidence: 99%

80K-H as a New Ca2+ Sensor Regulating the Activity of the Epithelial Ca2+ Channel Transient Receptor Potential Cation Channel V5 (TRPV5)

Gkika

Mahieu

Nilius

et al. 2004

Journal of Biological Chemistry

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binding. Electrophysiological studies using 80K-H mutants showed that three domains of 80K-H (the two EFhand structures, the highly acidic glutamic stretch, and the His-Asp-Glu-Leu sequence) are critical determinants for TRPV5 activity. Importantly, inactivation of the EFhand pair reduced the TRPV5-mediated Ca 2؉ current and increased the TRPV5 sensitivity to intracellular Ca 2؉ , accelerating the feedback inhibition of the channel. None of the 80K-H mutants altered the TRPV5 plasma membrane localization nor the association of 80K-H with TRPV5, suggesting that 80K-H has a direct effect on TRPV5 activity. In conclusion, we report a novel function for 80K-H as a Ca 2؉ sensor controlling TRPV5 channel activity.The maintenance of the body Ca 2ϩ balance is of crucial importance for many vital physiological functions, including neuronal excitability, muscle contraction, and bone formation.The recent identification of two novel members of the transient receptor potential (TRP) 1 superfamily, TRPV5 and TRPV6, has provided new insight into the molecular mechanisms controlling the extracellular Ca 2ϩ balance (1-3). TRPV5 and TRPV6 are Ca 2ϩ -selective channels involved in transcellular Ca 2ϩ transport across vitamin D 3 -sensitive epithelia, such as kidney, intestine, and placenta (4, 5). Furthermore, these two channels possess unique functional characteristics among the highly heterogeneous group of TRP channels (6). They exhibit a constitutively activated Ca 2ϩ permeability, a high Ca 2ϩ selectivity, and a Ca 2ϩ -dependent feedback mechanism regulating channel activity (7,8).TRPV5 activity is controlled by various regulatory mechanisms ranging from long-term transcriptional modulations to short-term direct physical interactions with intracellular factors. TRPV5 is regulated at the transcriptional level by 1,25-dihydroxyvitamin D 3 (1,25-(OH) 2 D 3 ), dietary Ca 2ϩ , and 17␤-estradiol (5, 9, 10). Previous studies have shown that these hormones and dietary Ca 2ϩ normalize the hypocalcemia in 25-hydroxyvitamin D 3 -1␣-hydroxylase knock-out mice, which is accompanied by an up-regulation of TRPV5 mRNA expression levels. Furthermore, TRPV5 modulation occurs at the post-translational level by controlling translocation of the channel from intracellular pools to the plasma membrane. Recently, the S100A10-annexin 2 complex was demonstrated to modulate the functional plasma membrane distribution of TRPV5 by direct association to the carboxyl (C)-terminal tail of the channel. Down-regulation of annexin 2 inhibited TRPV5-mediated currents in TRPV5-transfected cells (11). Finally, the terminal tails of the channel contain potential regulatory motifs, such as protein kinase C (PKC) phosphorylation sites, PDZ motifs, and ankyrin repeats (4). This suggests a regulatory role for the intracellular tails of TRPV5 in the (in)activation or the trafficking of the channel. In line with this observation, Niemeyer et al. (13) demonstrated that TRPV6 is competitively regulated by PKC and calmodulin.The aim of the present study was to identify ...

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Molecular Evolution of the Mammalian Alpha 2B Adrenergic Receptor

Cited by 25 publications

References 64 publications

Inferring Complex DNA Substitution Processes on Phylogenies Using Uniformization and Data Augmentation

Inferring Complex DNA Substitution Processes on Phylogenies Using Uniformization and Data Augmentation

Summary of Laurasiatheria (Mammalia) Phylogeny

80K-H as a New Ca2+ Sensor Regulating the Activity of the Epithelial Ca2+ Channel Transient Receptor Potential Cation Channel V5 (TRPV5)

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