Araştırma Makalesi
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Yıl 2021, Cilt: 4 Sayı: 2, 146 - 159, 30.11.2021
https://doi.org/10.34088/kojose.904914

Öz

Kaynakça

  • [1] Horiike T., Minai R., Miyata D., Nakamura Y., Tateno Y., 2016. Ortholog-Finder: A Tool for Constructing an Ortholog Data Set. Genome Biology and Evolution, 8, pp. 446-457.
  • [2] Soltis D.E., Soltis, P.S., 2003. The role of phylogenetics in comparative genetics. Plant physiology, 132, pp.1790–1800.
  • [3] Holder M., Lewis P.O., 2003. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews. Genetics, 4, pp. 275-84.
  • [4] Woese C.R., 2000. Interpreting the universal phylogenetic tree. Proceedings of the National Academy of Sciences of the United States of America, 97, pp. 8392–8396.
  • [5] BLM, Bloom syndrome RecQ like helicase. https://ghr.nlm.nih.gov/gene/BLM#location. Accessed October 20, 2020.
  • [6] Ding S.L., Yu J.C., Chen S. T., Hsu G.C., Kuo S.J., Lin Y.H., Wu P.E., Shen, C.Y., 2009. Genetic variants of BLM interact with RAD51 to increase breast cancer susceptibility. Carcinogenesis, 30, pp. 43–49.
  • [7] Shen M., Menashe I., Morton L.M., Zhang Y., Armstrong B., Wang S.S., Lan Q., Hartge P., Purdue M.P., Cerhan J.R., Grulich A., Cozen W., Yeager M., Holford T.R., Vajdic C.M., Davis S., Leaderer B., Kricker A., Severson R.K., Zahm S.H., Chatterjee N., Rothman N, Chanock S.J., Zheng T., 2010. Polymorphisms in DNA repair genes and risk of non-Hodgkin lymphoma in a pooled analysis of three studies. British journal of haematology, 151, pp. 239–244.
  • [8] Karow J.K., Constantinou A., Li J.L., West S.C., Hickson I.D., 2000. The Bloom's syndrome gene product promotes branch migration of holliday junctions. Proceedings of the National Academy of Sciences of the United States of America, 97, pp. 6504–6508.
  • [9] Frank B., Hoffmeister M., Klopp N., Illig T., Chang-Claude J., Brenner H., 2010. Colorectal cancer and polymorphisms in DNA repair genes WRN, RMI1 and BLM. Carcinogenesis, 31, pp. 442–445.
  • [10] Wang Z., Xu Y., Tang J., Ma H., Qin J., Lu C., Wang X., Hu Z., Wang X., Shen H., 2009. A polymorphism in Werner syndrome gene is associated with breast cancer susceptibility in Chinese women. Breast cancer research and treatment, 118, pp. 169–175.
  • [11] Broberg K., Huynh E., Schläwicke Engström K., Björk J., Albin M., Ingvar C., Olsson H., Höglund, M., 2009. Association between polymorphisms in RMI1, TOP3A, and BLM and risk of cancer, a case-control study. BMC cancer, 9, pp. 140.
  • [12] Vindigni A., Marino F., Gileadi, O., 2010. Probing the structural basis of RecQ helicase function. Biophysical Chemistry, 149, pp. 67–77.
  • [13] Pike A.C., Shrestha B., Popuri V., Burgess-Brown N., Muzzolini L., Constantini S., Vindigni A., Gileadi O., 2009. Structure of the human RECQ1 helicase reveals a putative strand-separation pin. Proceedings of the National Academy of Sciences of the United States of America, 27, pp. 1039-1044.
  • [14] Bernstein D.A., Zittel M.C., Keck J.L., 2003. High-resolution structure of the E.coli RecQ helicase catalytic core. The EMBO Journal, 22, pp. 4910–4921.
  • [15] Hoadley K.A., Keck J.L., 2010. Werner helicase wings DNA binding. Structure, 18, pp. 149–151.
  • [16] Beresten S.F., Stan R., van Brabant A.J., Ye, T., Naureckiene, S., Ellis, N. A., 1999. Purification of overexpressed hexahistidine-tagged BLM N431 as oligomeric complexes. Protein Expression and Purification, 17, pp. 239-248.
  • [17] Kim S.Y., Hakoshima T., Kitano K., 2013. Structure of the RecQ C-terminal domain of human Bloom syndrome protein. Scientific Reports, 21, pp. 3294.
  • [18] Fujikane R., Shinagawa H., Ishino Y., 2006. The archaeal Hjm helicase has recQ-like functions, and may be involved in repair of stalled replication fork. Genes to cells : devoted to molecular & cellular mechanisms, 11(2), pp. 99–110.
  • [19] Guy C.P., Bolt E.L., 2005. Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands. Nucleic acids research, 33(11), pp. 3678–3690.
  • [20] Fujikane R., Komori K., Shinagawa H., Ishino Y., 2005. Identification of a novel helicase activity unwinding branched DNAs from the hyperthermophilic archaeon, Pyrococcus furiosus. Journal of Biological Chemistry, 280(13), pp. 12351–12358.
  • [21] Li Z., Lu S., Hou G., Ma X., Sheng D., Ni, J., Shen Y., 2008. Hjm/Hel308A DNA helicase from Sulfolobus tokodaii promotes replication fork regression and interacts with Hjc endonuclease in vitro. Journal of bacteriology, 190(8), pp. 3006–3017.
  • [22] Hong Y., Chu M., Li Y., Ni J., Sheng D., Hou G., She Q., Shen Y., 2012. Dissection of the functional domains of an archaeal Holliday junction helicase. DNA Repair, 11(2), pp. 102-111.
  • [23] Liew L.P., Lim Z.Y., Cohen, M., Kong, Z., Marjavaara L., Chabes A., Bell, S.D., 2016. Hydroxyurea-Mediated Cytotoxicity Without Inhibition of Ribonucleotide Reductase. Cell reports, 17(6), pp. 1657–1670.
  • [24] Zhai B., DuPrez K., Han X., Yuan Z., Ahmad S., Xu C., Gu L., Ni J., Fan L., Shen Y., 2018. The archaeal ATPase PINA interacts with the helicase Hjm via its carboxyl terminal KH domain remodeling and processing replication fork and Holliday junction. Nucleic acids research, 46(13), pp. 6627–6641.
  • [25] Foster P.G., Hickey D.A., 1999. Computational bias may affect both DNA-based and protein based phylogenetic reconstructions. Journal of molecular evolution, 48(3), 284–290.
  • [26] Heath T.A., Huelsenbeck J.P., Stadler T., 2014. The fossilized birth-death process for coherent calibration of divergence-time estimates. Proceedings of the National Academy of Sciences of the United States of America, 111, pp. E2957-66.
  • [27] Felsenstein J., 1985. Confidence limits on phylogenies: an approach usingthe bootstrap. Evolution, 39, 783–791.
  • [28] Bagowski C.P., Bruins W., Te Velthuis A.J., 2010. The nature of protein domain evolution: shaping the interaction network. Current genomics, 11(5), 368–376.
  • [29] Mistry J., Chuguransky S., Williams L., Qureshi M., Salazar G.A., Sonnhammer E., Tosatto S., Paladin L., Raj S., Richardson L.J., Finn R.D., Bateman A., 2021. Pfam: The protein families database in 2021. Nucleic acids research, 49(D1),pp. D412–D419.
  • [30] Challa S., Neelapu N.R.R., 2019. Phylogenetic Trees: Applications, Construction, and Assessment. In: Hakeem K., Shaik N., Banaganapalli B., Elango R. (eds) Essentials of Bioinformatics, Volume III. Springer, Cham, Switzerland.
  • [31] Yokono M., Satoh S. Tanaka A., 2018. Comparative analyses of whole-genome protein sequences from multiple organisms. Scientific Reports, 8, pp. 6800.
  • [32] Opperdoes, F.R., 2003. Phylogenetic analysis using protein sequences. In The Phylogenetics Handbook: A Practical Approach to DNA and Protein Phylogeny, 1st ed. Salemi, M., Vandamme, A.-M., Eds., Cambridge University Press, Cambridge, London, United Kingdom.
  • [33] Bogdanowicz D., Giaro K., 2010. Comparing arbitrary unrooted phylogenetic trees using generalized matching split distance. 2nd International Conference on Information Technology, (2010 ICIT), Gdansk, Poland, pp. 259-262.
  • [34] Soltis P., Soltis, D., 2003. Applying the Bootstrap in Phylogeny Reconstruction. Statistical Science, 18(2), pp. 256-267.
  • [35] Varki A., Altheide T.K., 2005. Comparing the human and chimpanzee genomes: searching for needles in a haystack. Genome research, 15(12), pp. 1746–1758.
  • [36] Chen F.-C., Li W.-H., 2001. Genomic Divergences between Humans and Other Hominoids and the Effective Population Size of the Common Ancestor of Humans and Chimpanzees. The American Journal of Human Genetics, 68(2), pp. 444-456.
  • [37] Suntsova M.V., Buzdin A.A., 2020. Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species. BMC Genomics, 21, pp. 535.
  • [38] Chimpanzee Sequencing and Analysis Consortium, 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437(7055), pp. 69–87.
  • [39] Dorus S., Vallender E.J., Evans P.D., Anderson J.R., Gilbert S.L., Mahowald M., Wyckoff G.J., Malcom C.M., Lahn, B.T., 2004. Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell, 119(7), pp. 1027–1040.
  • [40] Evans P.D., Gilbert S.L., Mekel-Bobrov N., Vallender E.J., Anderson J.R., Vaez-Azizi L.M., Tishkoff S.A., Hudson R.R., Lahn B.T., 2005. Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science (New York, N.Y.), 309(5741), pp. 1717–1720.
  • [41] Zhang J., Webb D.M., Podlaha O., 2002. Accelerated protein evolution and origins of human-specific features: Foxp2 as an example. Genetics, 162(4), pp. 1825–1835.
  • [42] Wyckoff G.J., Wang W., Wu C.I., 2000. Rapid evolution of male reproductive genes in the descent of man. Nature, 403(6767), pp. 304–309.
  • [43] Go Y., Niimura Y., 2008. Similar numbers but different repertoires of olfactory receptor genes in humans and chimpanzees. Molecular biology and evolution, 25(9), pp. 1897–1907.
  • [44] Gallus S., Hallström B.M., Kumar V., Dodt W.G., Janke A., Schumann G.G., Nilsson, M.A., 2015. Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil. Molecular biology and evolution, 32(5), pp. 1268–1283.
  • [45] Kazazian H.H., Jr, Moran J.V., 2017. Mobile DNA in Health and Disease. The New England journal of medicine, 377(4), pp. 361–370.
  • [46] Wang P.J., 2017. Tracking LINE1 retrotransposition in the germline. Proceedings of the National Academy of Sciences of the United States of America, 114(28), pp. 7194–7196.
  • [47] Ostertag E.M., Kazazian H.H.,Jr, 2001. Biology of mammalian L1 retrotransposons. Annual review of genetics, 35, pp. 501–538.
  • [48] Peat J.R., Ortega-Recalde O., Kardailsky O., Hore, T.A., 2017. The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates. F1000Research, 6, pp. 526.
  • [49] Evolution, 2014. Scitable by Nature Education. https://www.nature.com/scitable/definition/evolution-78/. Accessed January 10, 2021.
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  • [51] Boto L., 2010. Horizontal gene transfer in evolution: facts and challenges. Proceedings. Biological sciences, 277(1683), pp. 819–827.
  • [52] Husnik F., McCutcheon J.P., 2018. Functional horizontal gene transfer from bacteria to eukaryotes. Nature reviews. Microbiology, 16(2), pp. 67–79.
  • [53] Naylor G.J.P., Brown W.M., 1998. Amplhioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Systematics Biology, 47, pp. 61–76.
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  • [55] Pavlov A.R., Belova G.I., Kozyavkin S.A., Slesarev, A.I., 2002. Helix-hairpin-helix motifs confer salt resistance and processivity on chimeric DNA polymerases. Proceedings of the National Academy of Sciences of the United States of America, 99(21), pp. 13510–13515.
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Searching for the Roots of Bloom Syndrome Protein and Its Homologs Using Phylogenetic Analysis

Yıl 2021, Cilt: 4 Sayı: 2, 146 - 159, 30.11.2021
https://doi.org/10.34088/kojose.904914

Öz

Phylogenetic analysis (PA) is used for elucidation of relationships among different species and provides information about their evolution. BLM protein (BLM RecQ like helicase) is responsible for the repair of stalled replication fork during double-strand break repair by homologous recombination. In the current study, phylogenetic analysis was performed using BLM protein sequences, sequences of its homologs and its putative homologs from 34 species including covering the genera of Bacteria, Archaea and Eukaryotes. This study was carried out for the purpose of (1) illustrating and comparing relationships among eukaryotic BLM proteins, their homologs (ATP-dependent DNA helicase RecQs in Bacteria) and their potential putative homologs (ATP-dependent DNA helicase Hel308s in Archaea), (2) evaluating how BLM protein evolution took place, what it brought to the organisms by acquiring functional changes and how future potential changes would occur and (3) gaining the general perspective in the evolution of BLM protein. All analyzed species in Bacteria, Archaea and Eukaryota formed a clear inter-species cluster, except for P. sinensis (Reptilia). The results supported that Hjm helicase may be one of the candidate potential ancestors of the BLM proteins and their homologs. Moreover, especially two domains which are Helicase ATP-binding and Helicase C-terminal domain were encountered in the all analyzed species and seem to be strictly conserved in the future. Repair related-highly sophisticated interaction network of BLM indicated that its functional evolution reaches a certain level and it appears to have taken an important place in maintaining genomic stability. However, it should be taken into account that BLM may acquire additional functions or become a cornerstone in different pathways in the future depending on its participation in various metabolic roads.

Kaynakça

  • [1] Horiike T., Minai R., Miyata D., Nakamura Y., Tateno Y., 2016. Ortholog-Finder: A Tool for Constructing an Ortholog Data Set. Genome Biology and Evolution, 8, pp. 446-457.
  • [2] Soltis D.E., Soltis, P.S., 2003. The role of phylogenetics in comparative genetics. Plant physiology, 132, pp.1790–1800.
  • [3] Holder M., Lewis P.O., 2003. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews. Genetics, 4, pp. 275-84.
  • [4] Woese C.R., 2000. Interpreting the universal phylogenetic tree. Proceedings of the National Academy of Sciences of the United States of America, 97, pp. 8392–8396.
  • [5] BLM, Bloom syndrome RecQ like helicase. https://ghr.nlm.nih.gov/gene/BLM#location. Accessed October 20, 2020.
  • [6] Ding S.L., Yu J.C., Chen S. T., Hsu G.C., Kuo S.J., Lin Y.H., Wu P.E., Shen, C.Y., 2009. Genetic variants of BLM interact with RAD51 to increase breast cancer susceptibility. Carcinogenesis, 30, pp. 43–49.
  • [7] Shen M., Menashe I., Morton L.M., Zhang Y., Armstrong B., Wang S.S., Lan Q., Hartge P., Purdue M.P., Cerhan J.R., Grulich A., Cozen W., Yeager M., Holford T.R., Vajdic C.M., Davis S., Leaderer B., Kricker A., Severson R.K., Zahm S.H., Chatterjee N., Rothman N, Chanock S.J., Zheng T., 2010. Polymorphisms in DNA repair genes and risk of non-Hodgkin lymphoma in a pooled analysis of three studies. British journal of haematology, 151, pp. 239–244.
  • [8] Karow J.K., Constantinou A., Li J.L., West S.C., Hickson I.D., 2000. The Bloom's syndrome gene product promotes branch migration of holliday junctions. Proceedings of the National Academy of Sciences of the United States of America, 97, pp. 6504–6508.
  • [9] Frank B., Hoffmeister M., Klopp N., Illig T., Chang-Claude J., Brenner H., 2010. Colorectal cancer and polymorphisms in DNA repair genes WRN, RMI1 and BLM. Carcinogenesis, 31, pp. 442–445.
  • [10] Wang Z., Xu Y., Tang J., Ma H., Qin J., Lu C., Wang X., Hu Z., Wang X., Shen H., 2009. A polymorphism in Werner syndrome gene is associated with breast cancer susceptibility in Chinese women. Breast cancer research and treatment, 118, pp. 169–175.
  • [11] Broberg K., Huynh E., Schläwicke Engström K., Björk J., Albin M., Ingvar C., Olsson H., Höglund, M., 2009. Association between polymorphisms in RMI1, TOP3A, and BLM and risk of cancer, a case-control study. BMC cancer, 9, pp. 140.
  • [12] Vindigni A., Marino F., Gileadi, O., 2010. Probing the structural basis of RecQ helicase function. Biophysical Chemistry, 149, pp. 67–77.
  • [13] Pike A.C., Shrestha B., Popuri V., Burgess-Brown N., Muzzolini L., Constantini S., Vindigni A., Gileadi O., 2009. Structure of the human RECQ1 helicase reveals a putative strand-separation pin. Proceedings of the National Academy of Sciences of the United States of America, 27, pp. 1039-1044.
  • [14] Bernstein D.A., Zittel M.C., Keck J.L., 2003. High-resolution structure of the E.coli RecQ helicase catalytic core. The EMBO Journal, 22, pp. 4910–4921.
  • [15] Hoadley K.A., Keck J.L., 2010. Werner helicase wings DNA binding. Structure, 18, pp. 149–151.
  • [16] Beresten S.F., Stan R., van Brabant A.J., Ye, T., Naureckiene, S., Ellis, N. A., 1999. Purification of overexpressed hexahistidine-tagged BLM N431 as oligomeric complexes. Protein Expression and Purification, 17, pp. 239-248.
  • [17] Kim S.Y., Hakoshima T., Kitano K., 2013. Structure of the RecQ C-terminal domain of human Bloom syndrome protein. Scientific Reports, 21, pp. 3294.
  • [18] Fujikane R., Shinagawa H., Ishino Y., 2006. The archaeal Hjm helicase has recQ-like functions, and may be involved in repair of stalled replication fork. Genes to cells : devoted to molecular & cellular mechanisms, 11(2), pp. 99–110.
  • [19] Guy C.P., Bolt E.L., 2005. Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands. Nucleic acids research, 33(11), pp. 3678–3690.
  • [20] Fujikane R., Komori K., Shinagawa H., Ishino Y., 2005. Identification of a novel helicase activity unwinding branched DNAs from the hyperthermophilic archaeon, Pyrococcus furiosus. Journal of Biological Chemistry, 280(13), pp. 12351–12358.
  • [21] Li Z., Lu S., Hou G., Ma X., Sheng D., Ni, J., Shen Y., 2008. Hjm/Hel308A DNA helicase from Sulfolobus tokodaii promotes replication fork regression and interacts with Hjc endonuclease in vitro. Journal of bacteriology, 190(8), pp. 3006–3017.
  • [22] Hong Y., Chu M., Li Y., Ni J., Sheng D., Hou G., She Q., Shen Y., 2012. Dissection of the functional domains of an archaeal Holliday junction helicase. DNA Repair, 11(2), pp. 102-111.
  • [23] Liew L.P., Lim Z.Y., Cohen, M., Kong, Z., Marjavaara L., Chabes A., Bell, S.D., 2016. Hydroxyurea-Mediated Cytotoxicity Without Inhibition of Ribonucleotide Reductase. Cell reports, 17(6), pp. 1657–1670.
  • [24] Zhai B., DuPrez K., Han X., Yuan Z., Ahmad S., Xu C., Gu L., Ni J., Fan L., Shen Y., 2018. The archaeal ATPase PINA interacts with the helicase Hjm via its carboxyl terminal KH domain remodeling and processing replication fork and Holliday junction. Nucleic acids research, 46(13), pp. 6627–6641.
  • [25] Foster P.G., Hickey D.A., 1999. Computational bias may affect both DNA-based and protein based phylogenetic reconstructions. Journal of molecular evolution, 48(3), 284–290.
  • [26] Heath T.A., Huelsenbeck J.P., Stadler T., 2014. The fossilized birth-death process for coherent calibration of divergence-time estimates. Proceedings of the National Academy of Sciences of the United States of America, 111, pp. E2957-66.
  • [27] Felsenstein J., 1985. Confidence limits on phylogenies: an approach usingthe bootstrap. Evolution, 39, 783–791.
  • [28] Bagowski C.P., Bruins W., Te Velthuis A.J., 2010. The nature of protein domain evolution: shaping the interaction network. Current genomics, 11(5), 368–376.
  • [29] Mistry J., Chuguransky S., Williams L., Qureshi M., Salazar G.A., Sonnhammer E., Tosatto S., Paladin L., Raj S., Richardson L.J., Finn R.D., Bateman A., 2021. Pfam: The protein families database in 2021. Nucleic acids research, 49(D1),pp. D412–D419.
  • [30] Challa S., Neelapu N.R.R., 2019. Phylogenetic Trees: Applications, Construction, and Assessment. In: Hakeem K., Shaik N., Banaganapalli B., Elango R. (eds) Essentials of Bioinformatics, Volume III. Springer, Cham, Switzerland.
  • [31] Yokono M., Satoh S. Tanaka A., 2018. Comparative analyses of whole-genome protein sequences from multiple organisms. Scientific Reports, 8, pp. 6800.
  • [32] Opperdoes, F.R., 2003. Phylogenetic analysis using protein sequences. In The Phylogenetics Handbook: A Practical Approach to DNA and Protein Phylogeny, 1st ed. Salemi, M., Vandamme, A.-M., Eds., Cambridge University Press, Cambridge, London, United Kingdom.
  • [33] Bogdanowicz D., Giaro K., 2010. Comparing arbitrary unrooted phylogenetic trees using generalized matching split distance. 2nd International Conference on Information Technology, (2010 ICIT), Gdansk, Poland, pp. 259-262.
  • [34] Soltis P., Soltis, D., 2003. Applying the Bootstrap in Phylogeny Reconstruction. Statistical Science, 18(2), pp. 256-267.
  • [35] Varki A., Altheide T.K., 2005. Comparing the human and chimpanzee genomes: searching for needles in a haystack. Genome research, 15(12), pp. 1746–1758.
  • [36] Chen F.-C., Li W.-H., 2001. Genomic Divergences between Humans and Other Hominoids and the Effective Population Size of the Common Ancestor of Humans and Chimpanzees. The American Journal of Human Genetics, 68(2), pp. 444-456.
  • [37] Suntsova M.V., Buzdin A.A., 2020. Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species. BMC Genomics, 21, pp. 535.
  • [38] Chimpanzee Sequencing and Analysis Consortium, 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437(7055), pp. 69–87.
  • [39] Dorus S., Vallender E.J., Evans P.D., Anderson J.R., Gilbert S.L., Mahowald M., Wyckoff G.J., Malcom C.M., Lahn, B.T., 2004. Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell, 119(7), pp. 1027–1040.
  • [40] Evans P.D., Gilbert S.L., Mekel-Bobrov N., Vallender E.J., Anderson J.R., Vaez-Azizi L.M., Tishkoff S.A., Hudson R.R., Lahn B.T., 2005. Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science (New York, N.Y.), 309(5741), pp. 1717–1720.
  • [41] Zhang J., Webb D.M., Podlaha O., 2002. Accelerated protein evolution and origins of human-specific features: Foxp2 as an example. Genetics, 162(4), pp. 1825–1835.
  • [42] Wyckoff G.J., Wang W., Wu C.I., 2000. Rapid evolution of male reproductive genes in the descent of man. Nature, 403(6767), pp. 304–309.
  • [43] Go Y., Niimura Y., 2008. Similar numbers but different repertoires of olfactory receptor genes in humans and chimpanzees. Molecular biology and evolution, 25(9), pp. 1897–1907.
  • [44] Gallus S., Hallström B.M., Kumar V., Dodt W.G., Janke A., Schumann G.G., Nilsson, M.A., 2015. Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil. Molecular biology and evolution, 32(5), pp. 1268–1283.
  • [45] Kazazian H.H., Jr, Moran J.V., 2017. Mobile DNA in Health and Disease. The New England journal of medicine, 377(4), pp. 361–370.
  • [46] Wang P.J., 2017. Tracking LINE1 retrotransposition in the germline. Proceedings of the National Academy of Sciences of the United States of America, 114(28), pp. 7194–7196.
  • [47] Ostertag E.M., Kazazian H.H.,Jr, 2001. Biology of mammalian L1 retrotransposons. Annual review of genetics, 35, pp. 501–538.
  • [48] Peat J.R., Ortega-Recalde O., Kardailsky O., Hore, T.A., 2017. The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates. F1000Research, 6, pp. 526.
  • [49] Evolution, 2014. Scitable by Nature Education. https://www.nature.com/scitable/definition/evolution-78/. Accessed January 10, 2021.
  • [50] Mozhayskiy V., Tagkopoulos I., 2012. Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution. BMC Bioinformatics, 13, pp. S13.
  • [51] Boto L., 2010. Horizontal gene transfer in evolution: facts and challenges. Proceedings. Biological sciences, 277(1683), pp. 819–827.
  • [52] Husnik F., McCutcheon J.P., 2018. Functional horizontal gene transfer from bacteria to eukaryotes. Nature reviews. Microbiology, 16(2), pp. 67–79.
  • [53] Naylor G.J.P., Brown W.M., 1998. Amplhioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Systematics Biology, 47, pp. 61–76.
  • [54] Xiong J., 2006. Protein Motifs and Domain Prediction. In Essential Bioinformatics (pp. 85-94). Cambridge: Cambridge University Press. Cambridge, London, United Kingdom.
  • [55] Pavlov A.R., Belova G.I., Kozyavkin S.A., Slesarev, A.I., 2002. Helix-hairpin-helix motifs confer salt resistance and processivity on chimeric DNA polymerases. Proceedings of the National Academy of Sciences of the United States of America, 99(21), pp. 13510–13515.
  • [56] Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P., 2002. Molecular Biology of the Cell. In DNA-Binding Motifs in Gene Regulatory Proteins. 4th ed. Garland Science, New York, USA.
  • [57] Newman J.A., Savitsky P., Allerston C.K., Bizard A.H., Özer Ö., Sarlós K., Liu Y., Pardon E., Steyaert J., Hickson I.D., Gileadi O., 2015. Crystal structure of the Bloom's syndrome helicase indicates a role for the HRDC domain in conformational changes. Nucleic acids research, 43(10), pp. 5221–5235.
  • [58] Shao X., Grishin N.V., 2000. Common fold in helix-hairpin-helix proteins. Nucleic acids research, 28(14), pp. 2643–2650.
  • [59] Umate P., Tuteja N., Tuteja R., 2011. Genome-wide comprehensive analysis of human helicases. Communicative & integrative biology, 4(1), pp. 118–137.
  • [60] Yankiwski V., Noonan J.P., Neff N.F., 2001. The C-terminal domain of the Bloom syndrome DNA helicase is essential for genomic stability. BMC cell biology, 2, pp. 11.
  • [61] Guo R.B., Rigolet P., Zargarian L., Fermandjian S., Xi X.G., 2005. Structural and functional characterizations reveal the importance of a zinc binding domain in Bloom's syndrome helicase. Nucleic acids research, 33(10), pp. 3109–3124.
  • [62] Shi J., Chen W.F., Zhang B., Fan S.H., Ai X., Liu N.N., Rety S., Xi X.G., 2017. A helical bundle in the N-terminal domain of the BLM helicase mediates dimer and potentially hexamer formation. The Journal of biological chemistry, 292(14), pp. 5909–5920.
  • [63] Manthei K.A., Keck, J.L., 2013. The BLM dissolvasome in DNA replication and repair. Cellular and molecular life sciences : CMLS, 70(21), pp. 4067–4084.
Toplam 63 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Yapısal Biyoloji
Bölüm Makaleler
Yazarlar

Tuğcan Korak 0000-0003-4902-4022

Murat Kasap 0000-0001-8527-2096

Yayımlanma Tarihi 30 Kasım 2021
Kabul Tarihi 11 Ağustos 2021
Yayımlandığı Sayı Yıl 2021 Cilt: 4 Sayı: 2

Kaynak Göster

APA Korak, T., & Kasap, M. (2021). Searching for the Roots of Bloom Syndrome Protein and Its Homologs Using Phylogenetic Analysis. Kocaeli Journal of Science and Engineering, 4(2), 146-159. https://doi.org/10.34088/kojose.904914