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201308Dec20:56

Secrets to ‘extreme adap­ta­tion’ found in Burmese python genome

Infor­ma­tion
pub­lished 08 Decem­ber 2013 | mod­i­fied 03 Novem­ber 2014
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The Burmese python’s abil­ity to ramp up its metab­o­lism and enlarge its organs to swal­low and digest prey whole can be traced to unusu­ally rapid evo­lu­tion and spe­cialised adap­ta­tions of its genes and the way they work, an inter­na­tional team of biol­o­gists says in a new paper.

Burmese pythonLead author Todd Cas­toe, an assis­tant pro­fes­sor of biol­ogy at The Uni­ver­sity of Texas at Arling­ton Col­lege of Sci­ence, and 38 co-​authors from four coun­tries sequenced and analysed the genome of the Burmese python (Python molu­rus bivit­ta­tus). Their paper is pub­lished online before print on 2 Decem­ber in the Pro­ceed­ings of the National Acad­emy of Sci­ences along with a com­pan­ion paper on the sequenc­ing and analy­sis of the king cobra (Ophio­ph­a­gus han­nah). The papers rep­re­sent the first com­plete and anno­tated snake genomes.

Because snakes con­tain many of the same genes as other ver­te­brates, study­ing how these genes have evolved to pro­duce such extreme and unique char­ac­ter­is­tics in snakes can even­tu­ally help explain how these genes func­tion, includ­ing how they enable extreme feats of organ remod­el­ling. Such knowl­edge may even­tu­ally be used to treat human diseases.

“One of the fun­da­men­tal ques­tions of evo­lu­tion­ary biol­ogy is how ver­te­brates with all the same genes dis­play such vastly dif­fer­ent char­ac­ter­is­tics. The Burmese python is a great way to study that because it is so extreme,” said Cas­toe, who began work­ing on the python project as a post­doc­toral fel­low at the Uni­ver­sity of Col­orado School of Med­i­cine in the lab­o­ra­tory of asso­ciate pro­fes­sor and paper cor­re­spond­ing author David D. Pollock.

We’d like to know how the snake uses genes we all have to do things that no other ver­te­brates can do.
Todd Cas­toe, lead author, Depart­ment of Biol­ogy, Uni­ver­sity of Texas, Arlington »

The new python study calls into ques­tion pre­vi­ous the­o­ries that major obvi­ous phys­i­cal dif­fer­ences among species are caused pri­mar­ily by changes in gene expres­sion. Instead, it con­tends that pro­tein adap­ta­tion, gene expres­sion and changes in the struc­ture of the organ­i­sa­tion of the genome itself are all at work together in deter­min­ing the unusual char­ac­ter­is­tics that define snakes, and pos­si­bly other vertebrates.

Pol­lock said the python and king cobra stud­ies rep­re­sent a sig­nif­i­cant addi­tion to the field of “com­par­a­tive sys­tems genomics — the evo­lu­tion­ary analy­sis of mul­ti­ple ver­te­brate genomes to under­stand how entire sys­tems of inter­act­ing genes can evolve from the mol­e­cules on up.” He said: “I believe that such stud­ies are going to be fun­da­men­tal to our abil­ity to under­stand what the genes in the human genome do, their func­tional mech­a­nisms, and how and why they came to be struc­tured the way they are.”

The Burmese python’s phe­no­type, or phys­i­cal char­ac­ter­is­tics, rep­re­sents one of the most extreme exam­ples of evo­lu­tion­ary adap­ta­tion, the authors said. Like all snakes, its evo­lu­tion­ary ori­gin included reduc­tion in func­tion of one lung and the elon­ga­tion of its mid-​section, skele­ton and organs. It also has an extra­or­di­nary abil­ity for what researchers call “phys­i­o­log­i­cal remodelling.”

Phys­i­o­log­i­cal remod­el­ling refers to the process by which pythons are able to digest meals much larger than their size, such as chick­ens or piglets, by ramp­ing up their metab­o­lism and increas­ing the mass of their heart, liver, small intes­tine and kid­neys 35 per­cent to 150 per­cent in only 24 to 48 hours. As the diges­tion is com­pleted, the organs return to their orig­i­nal size within a mat­ter of days. The authors sug­gest that under­stand­ing how snakes accom­plish these tremen­dous feats could hold vital clues for the devel­op­ment of treat­ments for many dif­fer­ent types of human diseases.

“The Burmese python has an amaz­ing phys­i­ol­ogy. With its genome in hand, we can now explore the many untapped mol­e­c­u­lar mech­a­nisms it uses to dra­mat­i­cally increase meta­bolic rate, to shut down acid pro­duc­tion, to improve intesti­nal func­tion, and to rapidly increase the size of its heart, intes­tine, pan­creas, liver and kid­neys,” said Stephen Secor, asso­ciate pro­fes­sor of bio­log­i­cal sci­ences at the Uni­ver­sity of Alabama and a co-​author on the paper. “The ben­e­fits of these dis­cov­er­ies tran­scends to the treat­ment of meta­bolic dis­eases, ulcers, intesti­nal mal­ab­sorp­tion, Crohn’s dis­ease, car­diac hyper­tro­phy and the loss of organ performance.”

Watch and hear the research team mem­bers explain about their work and the envis­aged poten­tial ben­e­fits:

To com­plete their work, the research team aligned 7,442 genes from the python and cobra with gene sequences avail­able in the Ensembl Genome Browser from other amphib­ians, rep­tile, bird and mam­mals. They used a sta­tis­ti­cal method called “branch site codon mod­el­ling” to look for genes that had been pos­i­tively selected (or evo­lu­tion­ar­ily changed due to nat­ural selec­tion) in the python, the cobra, and early in snake evo­lu­tion in the com­mon ances­tor of these two snakes. They found changes in hun­dreds of genes. They believe the results demon­strate that nat­ural selection-​driven changes in many genes that encode pro­teins con­tributed sub­stan­tially to the unique char­ac­ter­is­tics of snakes.

Analy­ses showed a remark­able cor­re­spon­dence between the func­tion of the selected genes, and the many func­tion­ally unique aspects of snake biol­ogy — such as their unique metab­o­lism, spine and skull shape and cell cycle reg­u­la­tion, Cas­toe said. Many of the altered genes the team observed also have promi­nent med­ical sig­nif­i­cance. For exam­ple, the python genome showed some changes to the gene GAB1, which other research sug­gests plays a role in breast can­cer, melanomas and child­hood leukemia.

In addi­tion to changes to indi­vid­ual genes and their expres­sion, researchers also found that the extreme char­ac­ter­is­tics in snakes could also be linked to dupli­ca­tions or losses in multi­gene fam­i­lies. Some of those include ancient loss and more recent re-​evolution of high res­o­lu­tion vision, and their abil­ity to detect chem­i­cal cues from the envi­ron­ment. Researchers also observed that, while most assume that rep­tile genes and genomes change at a very slow rate, snake genomes evolve at one of the fastest rates of any vertebrate.

See a fully grown python kill and eat a deer in this BBC Earth video, nar­rated by Sir David Atten­bor­ough:



(Source: Uni­ver­sity of Texas Arling­ton news release, 02.12.2013)


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