A Study of Mouse Genes for Major Urinary Proteins (MUPs)
November 8 2024 | Yehee Mun
Senior in high school from Holy Trinity High School writes a scientific research paper.
I. Abstract
This study explores the degree of difference of the Major Urinary Proteins in different mice strains. To observe this, I analyzed studies that organized the amino acid sequences of MUP genes in various mice strains and compared those MUP genes with other mice strains. This study concluded that MUP genes in different mice strains have almost identical amino acid sequences, resulting in a high degree of uniformity of MUP genes in different mice strains. This study aims to understand graft rejection in human transplantation in depth.
II. Introduction
Major Urinary Proteins, or MUP, are made in the livers and can be found in the urine of mice. MUP genes are highly polymorphic, which means each mouse’s genes have high variation, and each mouse has a distinctive scent chemical bound in the MUP structure's center pocket. Based on those diverse scent chemicals, mice are socially grouped. Today, MUP genes have evolved to function like Human Leukocyte Antigens by identifying each mouse with a unique gene. HLA genes are the genes that make each human unique, and those are known to be the most polymorphic genes that exist in humans. However, due to the high difference in HLA genes in each human, the risks of graft increase.
The biggest problem of graft is rejection. Graft rejection happens due to the HLA genes because the antibody recognizes something foreign by the difference of HLA genes. The graft rejection exists in all kinds of transplantations such as solid organ transplantation, cell transplantation, bone marrow transplantation, and more. Once the antibody notices foreign in our body, it attacks the foreign matter until it fails. To reduce the risk, patients receive donations only from donors that have matching blood types. Yet, this cannot relieve graft rejection completely. Currently, the only treatment for graft rejection is immunosuppressive drugs. These drugs suppress the immune system, therefore they cannot attack the transplant. However, immunosuppressive drugs increase the possibility of getting infections. According to the study done by Glenn et al. (2022) out of 2,388 participants, 15% had an experience of visiting a hospital due to infection at least once. (4) Thus, it is important to find how different HLA genes are from each human to decrease the risk of graft rejection.
The primary research question was whether different strains of mice exhibit varying amino acid sequences in their MUP proteins. The purpose of this study was for a better understanding of graft rejection by discovering the intensity of the difference in MUP genes between mice strains. Currently, it is unsure how much HLA genes differ in each human. Thus this study hopes to get some ideas for discovering HLA differences in each human and later on to find an ideal way of transplantation.
III. Research Hypothesis
MUP amino acid sequence differences correlate with distinct scent profiles, suggesting a high degree of variability in MUP amino acid sequences.
IV. Material and Methods
Materials:
1. Ensembl: Website that organizes annotated genomes
2. Clustal Omega: A website that performed Basic Local Alignment Search Tool analysis
3. A bar graph from “Diversity of major urinary proteins (MUPs) in wild house mice” by Michaela Thoß et al.
4. RCSB PDB: Website that organizes model structures
Methodology:
The study aimed to compare MUP amino acid sequences across different mouse strains. Initially, the study identified and performed BLAST analysis on 21 MUP gene amino acid sequences from the C57 strain using Ensembl, a website that organizes annotated genomes. To compare MUP gene diversity across 48 house mouse strains, the study used a bar graph from another study conducted by Michaela Thoß et al. Lastly, the study focused on MUP gene 5 to examine sequence variations among different mouse strains. The sequences were analyzed via Ensembl, and BLAST analysis was completed. This focus on MUP gene 5 was due to it being the most well-annotated MUP gene available for analysis.
V. Results and Data
Figure 1. Model Structure of the Mouse MUP Protein in Complex with a Scent Chemical
This model is a structure of the MUP gene 5. The red figure in the middle is a scent chemical bound inside a center pocket of MUP gene 5. The yellow figures around the scent chemical are part of the amino acid of the MUP gene 5 that lives close to the scent chemical.
Figure 2. 21 MUP Gene Alignment of the C57 Mice Strain
This alignment is based on 21 MUP genes from the C57 mice strain. Each row of the alignment depicts each MUP gene’s amino acid sequences by colors and letters. Thus, the different colors in a column mean some MUP genes have different amino sequences from other genes. This alignment shows that the 21 MUP genes from the C57 mice strain have identical amino acid sequences except for the red-boxed parts. This is important for this study since, Figure 4 is the analysis made only by MUP gene 5 from different mice strains, but the result would be similar among other MUP genes.
Figure 3. 48 House Mice MUP Gene Diversity, Number of alleles vs MUP Genes Found from House Mice
According to the study by Michaela Thoß et al, they captured 48 house mice and compared their MUP genes with other mice to determine the diversity of MUP genes from mice (Thoß, 2016). Figure 1 is the graph from Thoß’s study and the graph depicts that MUP gene 9 showed the highest diversity among different mice. This graph supports the hypothesis of this study by showing that 48 house mice have a high degree of difference in MUP genes.
Figure 4. MUP Gene 5 Alignment
This alignment is based on different mice strains' MUP gene 5 amino acid sequence. When a row has a consistent color code, it means that the amino acid sequences from different mice strains have identical sequences. For this study, except for the red-boxed part, each row from the alignment has identical color codes. This figure shows that MUP gene 5 from different mice strains has almost an identical amino acid sequence.
Figure 5. MUP Gene 5 Amino Acid Sequence Alignment
This alignment compares the amino acid sequence of five different mice strains. The letters on the left side show what kind of mice are used in the analysis and the numbers on the right side indicate how long those sequences are for each mouse strain. The punctuations that are written under the sequences depict where the alignments have a different letter of sequence. Colons and periods mean that the letters from the sequence are different, however, the stars mean that the letters from the sequence are equal. On the alignment, there are a total of 124 letters, and only 22 of those letters have different letters.
VI. Conclusion
The initial hypothesis of this study was that different mice strains may have a high percentage of MUP amino acid sequence differences. However, based on Figure 5, out of 124 letters, only 22 letters are different which is 16.80%. This revealed that the MUP amino acid sequences are almost identical among different mice strains. This finding suggests since mice share over 90% of DNA functions with humans, HLA genes may also show similar results: a high percentage of equality of HLA genes among humans. A deeper study of this could result in finding a way of reducing graft rejection after the transplantation and increasing survival.
One limitation of this study was that the studies that I used to analyze MUP amino acid sequences did not include all the data that were needed for this research. An example that was found during the research was that the website does not include the MUP genes of all mice strains. Compared to having well-annotated MUP genes of all mice strains, having fewer mice strains gives less certain results since this study is done based on less diverse information about MUP genes and mice strains.
Bibliography
Alelign, Tilahun, et al. “Kidney Transplantation: The Challenge of Human Leukocyte Antigen and Its Therapeutic Strategies.” PubMed, 5 March 2018, https://pubmed.ncbi.nlm.nih.gov/29693023/.
Choo, Sung Yoon. “The HLA system: genetics, immunology, clinical testing, and clinical implications.” PubMed, 28 February 2007, https://pubmed.ncbi.nlm.nih.gov/17326240/.
Cunningham, Fiona, et al. “Ensembl 2022.” Oxford Academic, 17 November 2021, https://academic.oup.com/nar/article/50/D1/D988/6430486.
Glenn, Dorey A., et al. “Immunosuppression Exposure and Risk of Infection-Related Acute Care Events in Patients With Glomerular Disease: An Observational Cohort Study.” PubMed, 1 October 2022, https://pubmed.ncbi.nlm.nih.gov/36339665/.
Thoß, Michaela, et al. “Diversity of major urinary proteins (MUPs) in wild house mice.” Scientific Reports, 6 December 2016, https://www.nature.com/articles/srep38378.
Zhou, Yingjiang, and Liangyou Rui. “Major Urinary Protein Regulation of Chemical Communication and Nutrient Metabolism.” NCBI, 2010, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034056/.