Human protamine 1 gene structure and function affected by rs35576928 mutation: a bioinformatics analysis

Suthar, Ramchandra; Kazemi, Elham

doi:10.22034/CAJMPSI.2021.05.02

Human protamine 1 gene structure and function affected by rs35576928 mutation: a bioinformatics analysis

Document Type : Research Paper

Authors

Ramchandra Suthar ¹
Elham Kazemi ²

¹ Department of Biotechnology, Pramukh Swami Science & H. D. Patel Arts College, Kadi, Gujarat, India

² Fertility and Infertility Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran

10.22034/CAJMPSI.2021.05.02

Abstract

Human sperm contain most type 1 and type 2 protamines (PRM1) and (PRM2), protamines, which have about equal proportions in normal sperm. Protamines can infertile if they change structure or function. Nucleotide polymorphisms are one cause of changes in protamine structure and function. For protamine 1 the genetic variation rs35576928 is known. In. this study bioinformatics approach was used to investigate the effects of the rs35576928 mutation on protamine 1 structure and function. matics tools including RNAsnp, NetGene2, in this study several bioinformatics tools were used to investigate how the polymorphism affects RNA structure and splicing. The tools used included RNAsnp, NetGene2, and ASAP. To evaluate the effects of rs35576928 on proteins, other tools such as SNAP and ExPASy were also used. The analyzes have also shown that this polymorphism has the primary, secondary and The results of this study have also shown that this polymorphism has primary, secondary, and the results of this study have also shown that this polymorphism has primary, secondary, and results of this study have also shown that protamine 1 has the following functions: general functions. Infertile males may be affected by rs35576928 as it has destructive effects on protamine RNA and protein structure.

Graphical Abstract

Highlights

Protamine is a vital protein for sperm structure and function.
There are two types of protamine in the structure of human sperm, usually in the same proportion as normal sperm.
Protamine 1 contains several polymorphisms that can affect its structure and function.
The polymorphism rs35576928 is an exonic variant that can affect the structure of the RNA and protein of protamine.

Keywords

Main Subjects

Bioinformatics

References

1. Balhorn R. The protamine family of sperm nuclear proteins. Gen Biol 2007; 8(9): 1-8.

https://doi.org/10.1186/gb-2007-8-9-227

CrossRef Google Scholar full-text PDF Mendeley PubMed PubMed Central

2. Oliva R. Protamines and male infertility. Hum Reprod Update 2006; 12(4): 417-435.

https://doi.org/10.1093/humupd/dml009

CrossRef Google Scholar full-text PDF Mendeley PubMed

3. Eirín-López JM, Frehlick LJ, Ausió J. Protamines, in the footsteps of linker histone evolution. J Biol Chem 2006; 281(1): 1-4.

https://doi.org/10.1074/jbc.R500018200

CrossRef Google Scholar full-text PDF Mendeley PubMed

4. Lewis JD, Song Y, de Jong ME, Bagha SM, Ausió J. A walk though vertebrate and invertebrate protamines. Chromosoma 2003; 111(8): 473-482.

https://doi.org/10.1007/s00412-002-0226-0

CrossRef Google Scholar full-text PDF Mendeley PubMed

5. Wyckoff GJ, Wang W, Wu CI. Rapid evolution of male reproductive genes in the descent of man. Nature 2000; 403(6767): 304-309.

https://doi.org/10.1038/35002070

CrossRef Google Scholar full-text PDF Mendeley

6. Amor H, Zeyad A, Hammadeh ME. Tobacco smoking and its impact on the expression level of sperm nuclear protein genes: H2BFWT, TNP1, TNP2, PRM1 and PRM2. Andrologia 2021; 53(3): e13964.

https://doi.org/10.1111/and.13964

CrossRef Google Scholar full-text PDF Mendeley PubMed

7. Choudhary SK, Wykes SM, Kramer JA, Mohamed AN, Koppitch F, Nelson JE, Krawetz SA. A haploid expressed gene cluster exists as a single chromatin domain in human sperm. J Biol Chem 1995; 270(15): 8755-8762.

https://doi.org/10.1074/jbc.270.15.8755

CrossRef Google Scholar full-text PDF Mendeley PubMed

8. Schlüter G, Engel W. The rat Prm3 gene is an intronless member of the protamine gene cluster and is expressed in haploid male germ cells. Cytogenet Genome Res 1995; 71(4): 352-355.

https://doi.org/10.1159/000134138

CrossRef Google Scholar full-text PDF Mendeley PubMed

9. Kramer JA, Krawetz SA. Genesis of a novel human sequence from the protamine PRM1 gene. Comp Biochem Physiol Pharm Toxicol Endocr 1998; 120(3): 467-473.

https://doi.org/10.1016/S0742-8413(98)10062-2

CrossRef Google Scholar full-text PDF Mendeley PubMed

10. Sarasa J, Enciso M, García L, Leza A, Steger K, Aizpurua J. Comparison of ART outcomes in men with altered mRNA protamine 1/protamine 2 ratio undergoing intracytoplasmic sperm injection with ejaculated and testicular spermatozoa. Asian J Androl 2020; 22(6): 623.

https://doi.org/10.4103/aja.aja_146_19

CrossRef Google Scholar full-text PDF Mendeley PubMed PubMed Central

11. Wu R, Liu C, Gu C, Hu X, Feng B, Chai B, Zhang Y. Characteristics of sod1 gene mutation in patients with amyotrophic lateral sclerosis and its relationship with clinical phenotype. Acta Medica Mediterr 2021; 37(2): 821-86.

https://doi.org/10.19193/0393-6384_2021_2_124

CrossRef Google Scholar full-text PDF Mendeley

12. Arauz-Garofalo G, Jodar M, Vilanova M, de la Iglesia Rodriguez A, Castillo J, Soler-Ventura A, Oliva R, Vilaseca M, Gay M. Protamine Characterization by Top-Down Proteomics: Boosting Proteoform Identification with DBSCAN. Proteomes 2021; 9(2): 21.

https://doi.org/10.3390/proteomes9020021

CrossRef Google Scholar full-text PDF Mendeley PubMed PubMed Central

13. Aoki VW, Carrell DT. Human protamines and the developing spermatid: their structure, function, expression and relationship with male infertility. Asian J Androl 2003; 5: 315-324.

CrossRef Google Scholar full-text PDF Mendeley PubMed

14. Tanaka H, Miyagawa Y, Tsujimura A, Matsumiya K, Okuyama A, Nishimune Y. Single nucleotide polymorphisms in the protamine-1 and -2 genes of fertile and infertile human male populations. Mol Hum Reprod 2003; 9: 69-73.

https://doi.org/10.1093/molehr/gag010

CrossRef Google Scholar full-text PDF Mendeley

15. He XJ, Ruan J, Du WD, Chen G, Zhou Y, Xu S, Zuo XB, Cao YX, Zhang XJ. PRM1 variant rs35576928 (Arg> Ser) is associated with defective spermatogenesis in the Chinese Han population. Reprod Biomed Online 2012; 25(6): 627-634.

https://doi.org/10.1016/j.rbmo.2012.09.005

CrossRef Google Scholar full-text PDF Mendeley PubMed

16. Lin P, Zhang Z, Chu J, Zhou Y, Li M, Yu W. Mir-182 affects nerve cell damage after epilepsy by regulating the expression of target gene apln. Acta Medica Mediterr 2021; 37(3): 1485-1490.

https://doi.org/10.19193/0393-6384_2021_3_237

CrossRef Google Scholar full-text PDF Mendeley

17. Ferlin A, Arredi B, Speltra E, Cazzadore C, Selice R, Garolla A, Lenzi A, Foresta C. Molecular and clinical characterization of Y chromosome microdeletions in infertile men: a 10-year experience in Italy. J Clin Endocr Metab 2007; 92(3): 762-770.

https://doi.org/10.1210/jc.2006-1981

CrossRef Google Scholar full-text PDF Mendeley PubMed

18. Yang M, Abdalrahman H, Sonia U, Mohammed AI, Vestine U, Wang M, Ebadi AG, Toughani M. The application of DNA molecular markers in the study of Codonopsis species genetic variation, a review. Cell Mol Biol 2020; 66(2): 23-30.

https://doi.org/10.14715/cmb/2020.66.2.3

CrossRef Google Scholar full-text PDF Mendeley PubMed

19. Zhoucun A, Zhang S, Yang Y, Ma Y, Zhang W, Lin L. The common variant N372H in BRCA2 gene may be associated with idiopathic male infertility with azoospermia or severe oligozoospermia. Eur J Obstet Gynecol Reprod Biol 2006; 124: 61-64.

https://doi.org/10.1016/j.ejogrb.2005.09.001

CrossRef Google Scholar full-text PDF Mendeley PubMed

20. Romanienko PJ, Camerini-Otero RD. Cloning, characterization, and localization of mouse and human SPO11. Genomics 1999; 61: 156-169.

https://doi.org/10.1006/geno.1999.5955

CrossRef Google Scholar full-text PDF Mendeley PubMed

21. Wu D, Yin X, Wang S, Yang L. Bilateral periventricular nodular heterotopia caused by a novel splicing mutation in the flna gene in a chinese family. Acta Medica Mediterr 2021; 37(2): 931-933.

https://doi.org/10.19193/0393-6384_2021_2_141

CrossRef Google Scholar full-text PDF Mendeley

22. Rovio AT, Marchington DR, Donat S, Schuppe HC, Abel J, Fritsche E, Elliott DJ, Laippala P, Ahola AL, McNay D, Harrison RF. Mutations at the mitochondrial DNA polymerase (POLG) locus associated with male infertility. Nat Genet 2001; 29(3): 261-262.

https://doi.org/10.1038/ng759

CrossRef Google Scholar full-text PDF Mendeley PubMed

23. Gromoll J, Simoni M. Genetic complexity of FSH receptor function. Trends Endocrinol Metab 2005; 16: 368-373.

https://doi.org/10.1016/j.tem.2005.05.011

CrossRef Google Scholar full-text PDF Mendeley PubMed

24. Abdallah WI, Hussein TM, Elsayed ET, Bahgat RS. The c.-190 C>A transversion in promoter region of protamine 1 gene as a genetic risk factor in Egyptian men with idiopathic infertility. Andrologia 2019; 51: e13367.

https://doi.org/10.1111/and.13367

CrossRef Google Scholar full-text PDF Mendeley PubMed

25. Patankar A, Parte P. Sperm chromatin compaction and male infertility. Male Infert Understand Causes Treat 2017: 295-315.

https://doi.org/10.1007/978-981-10-4017-7_17

CrossRef Google Scholar full-text PDF Mendeley

26. Jodar M, Oriola J, Mestre G, Castillo J, Giwercman A, Vidal‐Taboada JM, Ballesca JL, Oliva R. Polymorphisms, haplotypes and mutations in the protamine 1 and 2 genes. Int J Androl 2011; 34(5pt1): 470-485.

https://doi.org/10.1111/j.1365-2605.2010.01115.x

CrossRef Google Scholar full-text PDF Mendeley PubMed

27. Iguchi N, Yang S, Lamb DJ, Hecht NB. An SNP in protamine 1: a possible genetic cause of male infertility? J Med Genet 2006; 43: 382-384.

http://dx.doi.org/10.1136/jmg.2005.037168

CrossRef Google Scholar full-text PDF Mendeley PubMed PubMed Central

28. Ravel C, Chantot-Bastaraud S, El Houate B, Berthaut I, Verstraete L, De Larouziere V, Lourenco D, Dumaine A, Antoine JM, Mandelbaum J, Siffroi JP. Mutations in the protamine 1 gene associated with male infertility. Mol Hum Reprod 2007; 13(7): 461-464.

https://doi.org/10.1093/molehr/gam031

CrossRef Google Scholar full-text PDF Mendeley PubMed

29. Wen L, Zhang Y, Yang B, Han F, Ebadi AG, Toughani M. Knockdown of Angiopoietin-like protein 4 suppresses the development of colorectal cancer. Cell Mol Biol 2020; 66(5): 117-124.

https://doi.org/10.14715/cmb/2020.66.5.21

CrossRef Google Scholar full-text PDF Mendeley PubMed

30. Grassetti D, Paoli D, Gallo M, D’Ambrosio A, Lombardo F, Lenzi A, Gandini L. Protamine-1 and-2 polymorphisms and gene expression in male infertility: an Italian study. J Endocrinol Invest 2012; 35(10): 882-888.

https://doi.org/10.3275/8111

CrossRef Google Scholar full-text PDF Mendeley PubMed

31. Qu W, Huang W, Zhu GH, Wu Y, Kang Y, Hao S, Niu XL, Wang P. Four cases of nephropathy in children with coenzyme q10 deficiency induced by different gene mutations and literature review. Acta Medica Mediterr 2021; 37(1): 631-635.

https://doi.org/10.19193/0393-6384_2021_1_97

CrossRef Google Scholar full-text PDF Mendeley

32. Cho C, Jung-Ha H, Willis WD, Goulding EH, Stein P, Xu Z, Schultz RM, Hecht NB, Eddy EM. Protamine 2 deficiency leads to sperm DNA damage and embryo death in mice. Biol Reprod 2003; 69(1): 211-217.

https://doi.org/10.1095/biolreprod.102.015115

CrossRef Google Scholar full-text PDF Mendeley PubMed

33. Cho C, Willis WD, Goulding EH, Jung-Ha H, Choi YC, Hecht NB, Eddy EM. Haploinsufficiency of protamine-1 or-2 causes infertility in mice. Nat Genet 2001; 28(1): 82-86.

https://doi.org/10.1038/ng0501-82

CrossRef Google Scholar full-text PDF Mendeley PubMed

34. Carrell DT, Liu L. Altered protamine 2 expression is uncommon in donors of known fertility, but common among men with poor fertilizing capacity, and may reflect other abnormalities of spermiogenesis. J Androl 2001; 22: 604-610.

https://doi.org/10.1002/j.1939-4640.2001.tb02220.x

CrossRef Google Scholar full-text PDF Mendeley PubMed