Client’s Objective: The client sought to identify a protein encoded by a DNA sequence and analyze homologous proteins across different species, representing various biological groups such as mammals, birds, and rodents. The goal was to understand evolutionary relationships and functional significance across species.
Challenges: The client faced these challenges:
- Accurately identifying the protein encoded by the provided DNA sequence.
- Searching and filtering homologous proteins across various species.
- Conducting a comparative genomic analysis to understand evolutionary conservation.
Solution Provided:
1. Protein Identification: Using two different approaches, we identified the protein encoded by the DNA sequence:
- BlastX (NCBI): The sequence was uploaded and analyzed using default settings. The top hit was cofilin-1 (NP-005498.1) from Homo sapiens with 99% query coverage and 100% identity.
- SMS Translate: This tool was used to translate the DNA sequence, confirming the identification of the cofilin-1 protein.
2. Functional Analysis: We determined that cofilin-1 is involved in both building and breaking down actin filaments (F-actin and G-actin), crucial for cytoskeletal reorganization. Its function is pH-dependent and influenced by phosphorylation, particularly under the regulation of LIM kinase.
3. Homologous Protein Search: A comprehensive search for homologous proteins across multiple species was conducted. The search was filtered to include proteins from various taxonomic groups: rodents, bats, birds, cattle, worms, and yeast. Homologous proteins were identified using BlastX, and the top hits for each species were recorded.
4. Comparative Genomics:
- Multiple Sequence Alignment (MSA): Ten homologous sequences were selected for MSA using two different algorithms. These alignments were visually inspected, and trees were generated to analyze evolutionary relationships.
- Phylogenetic Tree Generation: The generated trees provided insights into the evolutionary conservation of cofilin-1 across species, showing high conservation among mammals and bats, while distant relationships were observed for birds and other taxa.
5. Statistical and Motif Analysis: We identified conserved and variable regions of the protein, and specific motifs were used to search against protein sequence databases, providing insights into the biological importance of these regions.
Outcome: The project successfully identified the cofilin-1 protein and mapped its homologs across multiple species. The comparative genomic analysis revealed the evolutionary conservation of key functional domains across taxa. The client was equipped with a comprehensive understanding of protein evolution and conservation, contributing to further research.
Tools and Technologies Used:
- Protein Identification: BlastX (NCBI), SMS Translate
- Functional Analysis: GenPept (NCBI)
- Homologous Protein Search: BlastX, NCBI databases
- Multiple Sequence Alignment: ClustalW, Muscle
- Phylogenetic Tree Generation: UPGMA, Maximum Likelihood Methods
- Statistical and Motif Analysis: MEME Suite, ScanProsite
This case study highlights our expertise in bioinformatics and comparative genomics, providing accurate protein identification, functional analysis, and evolutionary insights through advanced bioinformatics tools.
