EXAMINATION OF PSEUDOGENES FROM THE VIEWPOINTS OF EVOLUTION AND CREATION

Nüket ÇALIŞKAN1,  Prof. Dr. Hasan AKAN1, Çiğdem GÖVER1
1 Harran University, Faculty of Arts and Sciences, BiologyDepartment, Şanlıurfa.
[email protected]

What is Pseudogene?

Pseudogenes, which are called fake genes, are defined asgene-like regions of DNA that do not code a functional product and that have no duty. However, recent studies have shown that these genes have duties and that may play a role in the pathology of some diseases if they are developed.

Pseudogenes are known as gene-like regions that result from the duplication of a gene present in the genome. For many years, these genes were thought to be ‘junk DNA’ regions without any tasks. Pseudogenes were used by pro-evolution scientists as evidence of evolution. According to those scientists, the harmful mutation that disrupts the activity of the gene should be eliminated from the society through natural selection.However, pseudogenes are shown as an exception to it because the pseudogene is seen as a copy of an existing gene; in this case, the harmful mutation that occurs in one of the additional copies will not be eliminated because the other copy of the gene is already working. Consequently, the mutation in the additional copy will be transferred to the next generations. It is claimed that if any two species have the same pseudogenes and if those pseudogenes contain the same harmful mutations, they come from a common ancestor. The sharing of non-functional sequences and mutations is considered to be evidence of evolution.

Then,the following question comes to mind: “Why do the cells governed by the principle of minimum energy use so much energy to transfer those imitating genes, which have no function, to the next generation?”. For, according to creation, there is no room for the aimless genes in perfect creation. Pseudogenes must also have a purpose of creation. Indeed, recent molecular studies have shown that pseudogenes, which are thought to have no role for many years, have various tasks such as the regulation of mRNA stability and gene expression.

The pseudogenes’ having a duty is no different from other homologous structures in nature. All of this reflects the fact that the Creator uses the same "draft" or "art form" repeatedly when He builds different living beings. In thatcase, it is the duty of scientists to investigate and reveal the great engineering and harmony in creation.

DNA, that is, deoxyribonucleic acid, is the genetic material that carries the information necessary for the liveness and biological activities of all organisms and some viruses. The gene is the DNA region that allows a functional product such as polypeptide or RNA to be produced. [1] A gene region, a regulatory region called a promoter, and a termination codon that terminates the transcription are necessary for a functional product to form from the DNA region in a eukaryotic organism. After the gene region is transcribed from the DNA to primary RNAs with all parts, regions that will not be translated, such as the promoter, termination codon, intron, and, if present, the enhancer region, are removed. Finally, the exon regions are joined and mature mRNA is formed. Then, it is sent to ribosomes for amino acid synthesis. [2]

It is thought that those gene-like regions are caused by the duplication of an initially existing gene but that it subsequently lost its duty as a result of deletion, insertion, frame shift that prevents expression of the gene, or the accumulation of mutations forming a stop codon before normal time.

Pseudogenes first appeared in 1977 when Jacq et al. reported that there was a region in the genomic DNA sequence of Xenopus laevis, (African clawed frog)which is homologous to the gene that replicates 5S RNA, and that does not transcribe. [3] Later, it was demonstrated that these groups, whose transcription does not happen, existed in many living beings from prokaryotes to eukaryotes. [4] It is known that the human genome contains approximately 20,000 pseudogenes. [5] Although these pseudogenes show high homology in sequence as ancestral gene, they are regarded as the remnants of the genes that show homology because they somehow lost the ability to transcribe.

These genes are called pseudogenes, "false genes", based on the claim that these regions have no function. [6] However, recent studies have shown that these genes have duties and that may play a role in the pathology of some diseases if they are developed. [7]

Pseudogenes are divided into three groups according to the mechanism of formation (Figure 1):

  1. Unitary pseudogenes
  2. Duplicated pseudogenes
  3. Processed pseudogenes

It is thought that unitary pseudogenes were formed by the disruption of the transcription and translation mechanisms that enable the gene to form a functional product by accumulating random mutations in the ancestral gene. Pseudogenes in this group are called evolutionary waste or fossil genes by some scientists. Such pseudogenes occur when a single copy ancestor gene lose its function.[8]

Duplicated pseudogenes occur as a result of duplication of the ancestral gene. However, as a result of the duplication errors that occur during this duplication, the disruption of the gene’s enhancers and promoters, or themutation of the frame shift and the formation of early stop codon, the ability of the gene to transcribe is lost. Those pseudogenes are likely to be clustered on and near the same chromosome as the ancestral gene.[9]

As for processed pseudogenes, they are thought to formwhen the mRNA that forms as a result ofthe transcription of the ancestral gene is transformed into the cDNA with the reverse transcriptase enzyme and enters into the genome again. Since those pseudogenes are composed of mature mRNA, they do not contain introns and can also be located in areas away from the ancestral gene.[10]

Figure 1: The mechanism of pseudogene formation A. Unitary Pseudogenes, B. Duplicated Pseudogenes, C. Processed Pseudogenes.[11]

The View of Evolution

According to the view of evolution, mutations that disrupt the activity of the gene are eliminated from the society through natural selection. However, gene duplication is regarded as an exception because even if mutation occurs in the duplicated copy, natural selection will not take place because the other copy is already working and can meet the needs of the organism. That is, the duplicated gene containing the mutation can be transferred to other generations. The defective genes caused by harmful mutations in additional copies are also called pseudogenes. In other words, if any pseudogenes are found in any two species and if these pseudogenes are formed as a result of the same harmful mutations, it is shown as evidence that they come from a common ancestor. According to this view, the sharing of non-functional sequences and errors is defined as evolution. In addition, pseudogene sequences are considered genomic "fossils" in plant and animal genomes.

In a study, Ohta and Nishikimi compared the sequences of man, orangutan, chimpanzee, rat and macaque GULOP pseudogenes. At the end of the study, only 4 bases were found to be different among the GULOP pseudogenes containing around 120 nucleotides of man and chimpanzee. This difference is 8 nucleotides between man and orangutan (Figure 2). Acting upon this result, they suggested that the chimpanzee was closer to man.In short, chimpanzees, which we call apes, have a genome close to humans rather than another orangutan. In fact, according to this study, the animal with which we share the most pseudogenes is chimpanzee. A general picture is drawn showing that the shared genes and pseudogenes decrease as you go to other mammals, reptiles and fish.[12]

Figure 2: The comparison of GULOP pseudogene sequence of rat, man, chimpanzee, orangutan and macaque.[13]

The View of Creation

Everything in the cells and in the living body is extremely measured and calculated, and is carried out according to a plan and schedule. Such unnecessary, extra and waste materials are prepared to be used in another place by breaking down into the atoms in the cell.

According to the information above, those pseudogenes in many living groups insert themselves into DNA and are transferred from generation to generation. However, in that case, the following question comes to mind: “Why do the cells governed by the principle of minimum energy use so much energy to transfer those imitating genes, which have no function, to the next generation?”. [14]

However, there is no extra and redundant structure in the cell, not even an atom.Everything in the cells and in the living body is extremely measured and calculated, and is carried out according to a plan and schedule. Such unnecessary, extra and waste materials are prepared to be used in another place by breaking down into the atoms in the cell.

Pseudogenes have many different functions, such as mRNA regulation, increasing genetic diversity, reducing or increasing gene expression.

We need to go back a bit to understand the status of junk DNAs that are deemed to be non-functional. It was reported many years ago that only 3% of the DNA was necessary, and the remaining 97 percent were non-scientific and "insignificant". Biologists thought that DNA lost its function through evolution.

Similarly, it was claimed in the past that more than 80 structures and organs in humans were unnecessary vestigial organs and tissues. After that,those DNA sequences, whose duty we do not know, were considered insignificant.

However, according to the scientists who adopt the view of Creation, nothing can be purposeless in an organism that is perfectly designed and created. Everything that has been created must have a purpose. The fact that it has not been proved yet does not change this fact.

The pseudogenes are no different from other homologous structures in nature. All of this reflects the fact that the Creator uses the same "draft" or "art form" repeatedly when He builds different living beings. 

In that case, why pseudogenes exist and what their functions are should be investigated. As a matter of fact, recent studies have shown that pseudogenes are not purposeless and functionless genes but that they have a serious role in regulating the expression of genes. [15]

Pseudogenes have many different functions, such as mRNA regulation, increasing genetic diversity, reducing or increasing gene expression. For instance, the Oct4 gene, which has more than one pseudogene, acts as a transcription factor in stem cells, and one of the pseudogenes of this gene, overexpression of Oct4P, inhibits the differentiation of mesenchymal stem cells. [16]

A study involving bioinformatics techniques and experimental studies on genome basis was conducted by Chan et al in 2103. In this study, pseudogenes, target genes andesiRNAs were compared using the databases;it was found that the PPM1K gene, which is vital for cell survival and organ development, encodes esiRNA in the pseudogene, and that esiRNAs regulatethe expression of several genes including NEK8 gene, which is associated with cancer cell growth.

Experimental studies on 41 pairs of hepatocellular cancer tissues and normal tissue showed that PPM1K pseudogene in cancerous tissue decreased significantly compared to normal tissue while NCR8 expression increased.[17]

In a large-scale study conducted in 2012, 13 different cancer types and 293 tissue samples were studied and the activity of 2,082 different pseudogenes related to cancer was determined.[18]

Conclusion

It is impossible for any scientist or a worldwide consortium of scientists to test all those DNA base pairs one by one because the operation of DNA involves many different complex processes. To conclude that a DNA sequence has no function, it is necessary to test each base pair. It is an easy way of escape to call a DNA sequence "junk DNA, fake DNA" just because we do not know its duty.

The human genome consists of approximately 3 billion DNA base pairs. This long molecular code is responsible for the transformation of the cells that make up the human body into an adult cell from the zygote, and a development that lasts for decades. DNA has been assigned the task of controlling and managing all vital systems of the living being, and it has a very, very complicated structure.

Obviously, it is impossible for any scientist or a worldwide consortium of scientists to test all those DNA base pairs one by one because the operation of DNA involves many different complex processes. To conclude that a DNA sequence has no function, it is necessary to test each base pair. It isan easy way of escape to call a DNA sequence "junk DNA, fake DNA" just because we donot know its duty.

Instead, we should look at the genome from the perspective of widespread engagement and incredible bioengineering.Considering that there is nothing aimless in creation, we must work harder to discover the unknown things in the light of science.

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[1] Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 1953;171(4356):737-8.
[2] Kasap M. Gen İfadesinin Kontrolü. In: Kasap H, editor. Tibbi Biyoloji ve Genetik. Adana: Nobel Kitap Evi; 2010. p. 231-8.
[3] Jacq, C., Miller, J. R., & Brownlee, G. G. (1977). A pseudogene structure in 5S DNA of Xenopus laevis. Cell, 12(1), 109-120.
[4] Li, W., Yang, W., & Wang, X. J. (2013). Pseudogenes: pseudo or real functional elements?. Journal of genetics and genomics, 40(4), 171-177
[5] Han, Y. J., Ma, S. F., Yourek, G., Park, Y. D., & Garcia, J. G. (2011). A transcribed pseudogene of MYLK promotes cell proliferation. The FASEB Journal, 25(7), 2305-2312.
[6] Sönmez, D., Göğebakan, B., Ecevit, H., Ataç, L., Küçük, M. U., & İzmirli, M. (2016). Sahte İsmini Haketmeyen Genler; Psödogenler. Mustafa Kemal Üniversitesi Tıp Dergisi, 7(25).
[7] Tutar, Y. (2012). Pseudogenes. Comparative and functional genomics, 2012.
[8] Zhang, Z. D., Frankish, A., Hunt, T., Harrow, J., & Gerstein, M. (2010). Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome biology, 11(3), R26.
[9] Sönmez et al., 2016.ibid.
[10] Xiao-Jie, L., Ai-Mei, G., Li-Juan, J., & Jiang, X. (2015). Pseudogene in cancer: real functions and promising signature. Journal of medical genetics, 52(1), 17-24.
[11] Sönmez et al., 2016. ibid.
[12] Ohta, Y., & Nishikimi, M. (1999). Random nucleotide substitutions in primate nonfunctional gene for L-gulono-γ-lactone oxidase, the missing enzyme in L-ascorbic acid biosynthesis. Biochimica et Biophysica Acta (BBA)-General Subjects, 1472(1), 408-411.
[13] Ohta and Nishikimi, 1999. ibid.
[14] Pink RC, Wicks K, Caley DP, Punch EK, Jacobs L, Carter DR. Pseudogenes: pseudo-functional or key regulators in health and disease? Rna. 2011;17(5):792-8.
[15] Tutar, Y. (2012). ibid.
[16] Lin H, Shabbir A, Molnar M, Lee T. Stem cell regulatory function mediated by expression of a novel mouse Oct4 pseudogene. Biochemical and biophysical research communications. 2007;355(1):111-6.
[17] Chan, W. L., Yuo, C. Y., Yang, W. K., Hung, S. Y., Chang, Y. S., Chiu, C. C., ... & Chang, J. G. (2013). Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular  carcinoma. Nucleic acids research, 41(6), 3734-3747.
[18] Kalyana-Sundaram, S., Kumar-Sinha, C., Shankar, S., Robinson, D. R., Wu, Y. M., Cao, X., ... & Iyer, M. K. (2012). Expressed pseudogenes in the transcriptional landscape of human cancers. Cell, 149(7), 1622-1634.

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