Episodes of Rapid Recovery of the Functional Activity of the Gene in the Evolutionary History of Phylogenetically Distant Species

Overview

Journal Front Genet

Date 2022 Jan 31

PMID 35096018

Authors

A I Chekunova

S Yu Sorokina

E A Sivoplyas

G N Bakhtoyarov

P A Proshakov

A V Fokin

A I Melnikov

A M Kulikov

Affiliations

Soon will be listed here.

Abstract

As assemblies of genomes of new species with varying degrees of relationship appear, it becomes obvious that structural rearrangements of the genome, such as inversions, translocations, and transposon movements, are an essential and often the main source of evolutionary variation. In this regard, the following questions arise. How conserved are the regulatory regions of genes? Do they have a common evolutionary origin? And how and at what rate is the functional activity of genes restored during structural changes in the promoter region? In this article, we analyze the evolutionary history of the formation of the regulatory region of the gene in different lineages of the genus , as well as the participation of mobile elements in structural rearrangements and in the replacement of specific areas of the promoter region with those of independent evolutionary origin. In the process, we substantiate hypotheses about the selection of promoter elements from a number of frequently repeated motifs with different degrees of degeneracy in the ancestral sequence, as well as about the restoration of the minimum required set of regulatory sequences using a conversion mechanism or similar.

References

Tamura K . Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol. 1992; 9(4):678-87. DOI: 10.1093/oxfordjournals.molbev.a040752. View

Spradling A, Stern D, Beaton A, Rhem E, Laverty T, Mozden N . The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes. Genetics. 1999; 153(1):135-77. PMC: 1460730. DOI: 10.1093/genetics/153.1.135. View

Hedges D, Deininger P . Inviting instability: Transposable elements, double-strand breaks, and the maintenance of genome integrity. Mutat Res. 2006; 616(1-2):46-59. PMC: 1850990. DOI: 10.1016/j.mrfmmm.2006.11.021. View

Stormo G . Modeling the specificity of protein-DNA interactions. Quant Biol. 2014; 1(2):115-130. PMC: 4101922. DOI: 10.1007/s40484-013-0012-4. View

Parks A, Cook K, Belvin M, Dompe N, Fawcett R, Huppert K . Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome. Nat Genet. 2004; 36(3):288-92. DOI: 10.1038/ng1312. View

Rose R, Golosova O, Sukhomlinov D, Tiunov A, Prosperi M . Flexible design of multiple metagenomics classification pipelines with UGENE. Bioinformatics. 2018; 35(11):1963-1965. DOI: 10.1093/bioinformatics/bty901. View

Galhardo R, Hastings P, Rosenberg S . Mutation as a stress response and the regulation of evolvability. Crit Rev Biochem Mol Biol. 2007; 42(5):399-435. PMC: 3319127. DOI: 10.1080/10409230701648502. View

Kovalenko L, Zakharenko L, Voloshina M, Karamysheva T, Rubtsov N, Zakharov I . [Behavior of hobo and P transposons in yellow2-717 unstable line of Drosophila melanogaster and its derivatives after crossing with a laboratory strain]. Genetika. 2006; 42(6):748-56. View

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

10.

Rojas A, Fuentes G, Rausell A, Valencia A . The Ras protein superfamily: evolutionary tree and role of conserved amino acids. J Cell Biol. 2012; 196(2):189-201. PMC: 3265948. DOI: 10.1083/jcb.201103008. View

11.

Rach E, Yuan H, Majoros W, Tomancak P, Ohler U . Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biol. 2009; 10(7):R73. PMC: 2728527. DOI: 10.1186/gb-2009-10-7-r73. View

12.

Alonso-Gonzalez L, Dominguez A, Albornoz J . Direct determination of the influence of extreme temperature on transposition and structural mutation rates of Drosophila melanogaster mobile elements. Genetica. 2006; 128(1-3):11-9. DOI: 10.1007/s10709-005-2480-6. View

13.

Lankenau D . Genetics of genetics in Drosophila: P elements serving the study of homologous recombination, gene conversion and targeting. Chromosoma. 1995; 103(10):659-68. DOI: 10.1007/BF00344226. View

14.

Zelentsova H, Poluectova H, Mnjoian L, Lyozin G, Veleikodvorskaja V, Zhivotovsky L . Distribution and evolution of mobile elements in the virilis species group of Drosophila. Chromosoma. 2000; 108(7):443-56. DOI: 10.1007/s004120050396. View

15.

Velandia-Huerto C, Berkemer S, Hoffmann A, Retzlaff N, Romero Marroquin L, Hernandez-Rosales M . Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies. BMC Genomics. 2016; 17(1):617. PMC: 4981973. DOI: 10.1186/s12864-016-2927-4. View

16.

Wu Y, Zhuang Y, Han M, Xu T, Deng K . Ras promotes cell survival by antagonizing both JNK and Hid signals in the Drosophila eye. BMC Dev Biol. 2009; 9:53. PMC: 2773777. DOI: 10.1186/1471-213X-9-53. View

17.

Grant C, Bailey T, Noble W . FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011; 27(7):1017-8. PMC: 3065696. DOI: 10.1093/bioinformatics/btr064. View

18.

Pomerantseva E, Biryukova I, Silicheva R, Savitskaya E, Golovnin A, Georgiev P . Transposition of Regulatory Elements by P-Element-Mediated Rearrangements in Drosophila melanogaster. Genetics. 2006; 172(4):2283-91. PMC: 1456364. DOI: 10.1534/genetics.105.052803. View

19.

Chen E, Tan C, Kou Y, Duan Q, Wang Z, Meirelles G . Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013; 14:128. PMC: 3637064. DOI: 10.1186/1471-2105-14-128. View

20.

Chen J, Cooper D, Chuzhanova N, Ferec C, Patrinos G . Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet. 2007; 8(10):762-75. DOI: 10.1038/nrg2193. View