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The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

ABSTRACT: Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.

SUBMITTER: Castoe TA

PROVIDER: S-EPMC3870669 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature

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The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

Castoe Todd A TA de Koning A P Jason AP Hall Kathryn T KT Card Daren C DC Schield Drew R DR Fujita Matthew K MK Ruggiero Robert P RP Degner Jack F JF Daza Juan M JM Gu Wanjun W Reyes-Velasco Jacobo J Shaney Kyle J KJ Castoe Jill M JM Fox Samuel E SE Poole Alex W AW Polanco Daniel D Dobry Jason J Vandewege Michael W MW Li Qing Q Schott Ryan K RK Kapusta Aurélie A Minx Patrick P Feschotte Cédric C Uetz Peter P Ray David A DA Hoffmann Federico G FG Bogden Robert R Smith Eric N EN Chang Belinda S W BS Vonk Freek J FJ Casewell Nicholas R NR Henkel Christiaan V CV Richardson Michael K MK Mackessy Stephen P SP Bronikowski Anne M AM Yandell Mark M Warren Wesley C WC Secor Stephen M SM Pollock David D DD

Proceedings of the National Academy of Sciences of the United States of America 20131202 51

Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insigh ...[more]

PMID: 24297902

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Project description:BACKGROUND: Vertebrate predators use a broad arsenal of behaviors and weaponry for overcoming fractious and potentially dangerous prey. A unique array of predatory strategies occur among snakes, ranging from mechanical modes of constriction and jaw-holding in non-venomous snakes, to a chemical means, venom, for quickly dispatching prey. However, even among venomous snakes, different prey handling strategies are utilized, varying from the strike-and-hold behaviors exhibited by highly toxic elapid snakes to the rapid strike-and-release envenomation seen in viperid snakes. For vipers, this mode of envenomation represents a minimal risk predatory strategy by permitting little contact with or retaliation from prey, but it adds the additional task of relocating envenomated prey which has wandered from the attack site. This task is further confounded by trails of other unstruck conspecific or heterospecific prey. Despite decades of behavioral study, researchers still do not know the molecular mechanism which allows for prey relocation. RESULTS: During behavioral discrimination trials (vomeronasal responsiveness) to euthanized mice injected with size-fractionated venom, Crotalus atrox responded significantly to only one protein peak. Assays for enzymes common in rattlesnake venoms, such as exonuclease, L-amino acid oxidase, metalloproteinase, thrombin-like and kallikrein-like serine proteases and phospholipase A(2), showed that vomeronasal responsiveness was not dependent on enzymatic activity. Using mass spectrometry and N-terminal sequencing, we identified the proteins responsible for envenomated prey discrimination as the non-enzymatic disintegrins crotatroxin 1 and 2. Our results demonstrate a novel and critical biological role for venom disintegrins far beyond their well-established role in disruption of cell-cell and cell-extracellular matrix interactions. CONCLUSIONS: These findings reveal the evolutionary significance of free disintegrins in venoms as the molecular mechanism in vipers allowing for effective relocation of envenomated prey. The presence of free disintegrins in turn has led to evolution of a major behavioral adaptation (strike-and-release), characteristic of only rattlesnakes and other vipers, which exploits and refines the efficiency of a pre-existing chemical means of predation and a highly sensitive olfaction system. This system of a predator chemically tagging prey represents a novel trend in the coevolution of predator-prey relationships.

Dataset Information

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

Publications

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

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