Erratum: Genome analysis of the platypus reveals unique signatures of evolution

Warren, Wesley C.; Hillier, La Deana W.; Graves, Jennifer A. Marshall; Birney, Ewan; Ponting, Chris P.; Grützner, Frank; Belov, Katherine; Miller, Webb; Clarke, Laura; Chinwalla, Asif T.; Yang, Shiaw Pyng; Heger, Andreas; Locke, Devin P.; Miethke, Pat; Waters, Paul D.; Veyrunes, Frédéric; Fulton, Lucinda A.; Fulton, Bob; Graves, Tina; Wallis, John W.; Puente, Xosé S.; López-Otı́n, Carlos; Ordó̃ez, Gonzalo R.; Eichler, Evan E.; Chen, Lin; Cheng, Ze; Deakin, Janine E.; Alsop, Amber E.; Thompson, Katherine; Kirby, Patrick J.; Papenfuss, Anthony T.; Wakefield, Matthew J.; Olender, Tsviya; Lancet, Doron; Huttley, Gavin A.; Smit, Arian F. A.; Pask, Andrew J; Temple-Smith, Peter; Batzer, Mark A.; Walker, Jerilyn A.; Konkel, Miriam K.; Harris, Robert S.; Whittington, Camilla M.; Wong, Emily S.; Gemmell, Neil J.; Buschiazzo, Emmanuel; Jentzsch, Iris M. Vargas; Merkel, Angelika; Schmitz, Juergen; Zemann, Anja; Churakov, Gennady; Kriegs, Jan Ole; Brosius, Juergen; Murchison, Elizabeth P.; Sachidanandam, Ravi; Smith, Cristine; Hannon, Gregory J.; Tsend-Ayush, Enkhjargal; McMillan, Daniel A.; Attenborough, Rosalind; Rens, Willem; Ferguson-Smith, Malcolm; Lefèvre, Christophe; Sharp, Julie A.; Nicholas, Kevin R.; Ray, David A.; Kube, Michael; Reinhardt, Richard; Pringle, Thomas H.; Taylor, James G.; Jones, Russell C.; Nixon, Brett; Dacheux, J. L.; Niwa, Hitoshi; Sekita, Yoko; Huang, Xiaoqiu; Stark, Alexander; Kheradpour, Pouya; Kellis, M; Flicek, Paul; Chen, Yuan; Webber, Caleb; Hardison, Ross C.; Nelson, Joanne O.; Hallsworth-Pepin, Kym; Delehaunty, Kim D.; Markovic, Chris; Minx, Pat; Feng, Yucheng; Kremitzki, Colin; Mitreva, Makedonka; Glasscock, Jarret; Wylie, Todd; Wohldmann, Patricia; Thiru, Prathapan; Nhan, Michael N.; Pohl, Craig; Smith, Scott M.; Hou, Shunfeng; Nefedov, Mikhail; Jong, Pieter J. de; Renfree, Marilyn B.; Mardis, Elaine R.; Wilson, Richard K.

doi:10.1038/nature07253

Cited by 43 publications

(75 citation statements)

References 1 publication

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“…A mosaic of derived and plesiomorphic characters in monotremes, as exemplified by our analysis of the echidna rhodopsin sequence, has also been reported from anatomic, genomic, physiological, and developmental studies (Bolk et al, 1934;Gresser & Noback, 1935;Griffiths, 1989;Young & Pettigrew, 1991;Warren et al, 2008;Werneburg & Sánchez-Villagra, 2010). This aspect of the echidna rhodopsin sequence would support the yet controversial Theria hypothesis that monotremes are sister to marsupials and placentals (Janke et al, 2002;Rowe et al, 2008).…”

Section: Echidna Rhodopsin Sequence Analysissupporting

confidence: 85%

Functional characterization of the rod visual pigment of the echidna (Tachyglossus aculeatus), a basal mammal

et al. 2012

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Monotremes are the most basal egg-laying mammals comprised of two extant genera, which are largely nocturnal. Visual pigments, the first step in the sensory transduction cascade in photoreceptors of the eye, have been examined in a variety of vertebrates, but little work has been done to study the rhodopsin of monotremes. We isolated the rhodopsin gene of the nocturnal short-beaked echidna (Tachyglossus aculeatus) and expressed and functionally characterized the protein in vitro. Three mutants were also expressed and characterized: N83D, an important site for spectral tuning and metarhodopsin kinetics, and two sites with amino acids unique to the echidna (T158A and F169A). The k max of echidna rhodopsin (497.9 6 1.1 nm) did not vary significantly in either T158A (498.0 6 1.3 nm) or F169A (499.4 6 0.1 nm) but was redshifted in N83D (503.8 6 1.5 nm). Unlike other mammalian rhodopsins, echidna rhodopsin did react when exposed to hydroxylamine, although not as fast as cone opsins. The retinal release rate of light-activated echidna rhodopsin, as measured by fluorescence spectroscopy, had a half-life of 9.5 6 2.6 min À1 , which is significantly shorter than that of bovine rhodopsin. The half-life of the N83D mutant was 5.1 6 0.1 min À1 , even shorter than wild type. Our results show that with respect to hydroxylamine sensitivity and retinal release, the wild-type echidna rhodopsin displays major differences to all previously characterized mammalian rhodopsins and appears more similar to other nonmammalian vertebrate rhodopsins such as chicken and anole. However, our N83D mutagenesis results suggest that this site may mediate adaptation in the echidna to dim light environments, possibly via increased stability of light-activated intermediates. This study is the first characterization of a rhodopsin from a most basal mammal and indicates that there might be more functional variation in mammalian rhodopsins than previously assumed.

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Section: Echidna Rhodopsin Sequence Analysissupporting

confidence: 85%

Functional characterization of the rod visual pigment of the echidna (Tachyglossus aculeatus), a basal mammal

et al. 2012

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“…In chicken OC-116, a dentonin region is lacking, but a SGDG motif exists. Although MEPE/OC-116 probably inherited a SGDG motif from their amniote ancestor, the event creating the dentonin region seems to have occurred in the common ancestor of placentals, after the divergence of marsupials, some 148 Ma [36]. This typical feature was secondary kept unchanged in placentals as probably improving MEPE function.…”

Section: Dentonin Regionmentioning

confidence: 86%

“…Taken together, these data indicate (1) a dual function for MEPE/OC-116 in bone and eggshell mineralization in the chick, and (2) the presence of MEPE/OC-116 in the genome of the common amniote ancestor (mammals and sauropsids). The platypus, whose lineage ancestor is supposed to have diverged from an ancestral Theria approximately 160 Ma [36], possesses both mammalian (hair, milk) and sauropsid features (cleidoic eggs). Platypus eggs are encased within a parchment-like shell, which has a crystalline component [37].…”

Section: Positive Selectionmentioning

confidence: 99%

MEPE evolution in mammals reveals regions and residues of prime functional importance

Bardet¹,

Delgado²,

Sire

2009

Cell. Mol. Life Sci.

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In mammals, the matrix extracellular phosphoglycoprotein (MEPE) is known to activate osteogenesis and mineralization via a particular region called dentonin, and to inhibit mineralization via its ASARM (acidic serine-aspartate rich MEPE-associated motif) peptide that also plays a role in phosphatemia regulation. In order to understand MEPE evolution in mammals, and particularly that of its functional regions, we conducted an evolutionary analysis based on the study of selective pressures. Using 37 mammalian sequences we: (1) confirmed the presence of an additional coding exon in most placentals; (2) highlighted several conserved residues and regions that could have important functions; (3) found that dentonin function was recruited in a placental ancestor; and (4) revealed that ASARM function was present earlier, pushing the recruitment of MEPE deep into amniote origins. Our data indicate that MEPE was involved in various functions (bone and eggshell mineralization) prior to acquiring those currently known in placental mammals.

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“…Relying on degenerate polymerase chain reaction (PCR), a novel experimental strategy at that time, Buck and Axel identified a diverse family of approximately 1,000 genes in the rat olfactory epithelium. Subsequent studies have led to the identification of the OR gene family in numerous additional species, including human [4][5][6][7], mouse [4,6,[8][9][10], fish [11,12], nematode [13], fruit fly [14][15][16][17], mosquito [18], red flour beetle [19,20], honeybee [21], and platypus [22]. Vertebrate OR genes comprise the largest family of G protein-coupled receptors (GPCRs) [23].…”

Section: Introductionmentioning

confidence: 99%

Mammalian olfactory receptors: pharmacology, G protein coupling and desensitization

Kato

Touhara

2009

Cell. Mol. Life Sci.

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The vertebrate olfactory system recognizes and discriminates between thousands of structurally diverse odorants. Detection of odorants in mammals is mediated by olfactory receptors (ORs), which comprise the largest superfamily of G protein-coupled receptors (GPCRs). Upon odorant binding, ORs couple to G proteins, resulting in an increase in intracellular cAMP levels and subsequent receptor signaling. In this review, we will discuss recently published studies outlining the molecular basis of odor discrimination, focusing on pharmacology, G protein activation, and desensitization of ORs. A greater understanding of the molecular mechanisms underlying OR activity may help in the discovery of agonists and antagonists of ORs, and of GPCRs with potential therapeutic applications.

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Erratum: Genome analysis of the platypus reveals unique signatures of evolution

Cited by 43 publications

References 1 publication

Functional characterization of the rod visual pigment of the echidna (Tachyglossus aculeatus), a basal mammal

Functional characterization of the rod visual pigment of the echidna (Tachyglossus aculeatus), a basal mammal

MEPE evolution in mammals reveals regions and residues of prime functional importance

Mammalian olfactory receptors: pharmacology, G protein coupling and desensitization

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