Skripsi

Analisis terhadap Sekuens Gen ABC1 Pengode Resistansi Azol pada Candida krusei = Analysis of Azole Resistance Coder Gene Sequence ABC1 in Candida krusei.

Latar belakang: Candida adalah genus ragi penyebab kandidiasis. Penyakit ini memiliki tingkat morbiditas dan mortalitas yang tinggi terutama pada pasien immunocompromised. Candida penyebab kandidiasis terbanyak adalah C. albicans. Namun, angka kejadian kandidiasis oleh spesies non-albicans (NAC) mulai naik. Salah satu penyebab NAC adalah C. krusei. Spesies ini secara alami resistan terhadap flukonazol. Salah satu faktor resistansi ini adalah protein transpor ATP-binding cassette 1 (Abc1p) yang dikode gen ABC1. Analisis terhadap gen ABC1 dan Abc1p diharapkan dapat memberikan pemahaman lebih baik terhadap mekanisme resistansi C. krusei Metode: Penelitian eksperimental observasional ini melihat karakteristik protein Abc1p dari whole-genome sequence (WGS) 16 spesimen C. krusei yang diunggah ke database NCBI. Sekuens gen ABC1 dari spesimen dicari dengan membandingkannya dengan gen ABC1 C. krusei lain di database NCBI dan UniProtKB menggunakan BLAST. Homolog protein Abc1p dicari pada spesies Candida lainnya di database NCBI menggunakan BLAST. Analisis filogeni Abc1p C. krusei dengan Candida lainnya dilakukan dengan MEGA11. Prediksi efek perubahan asam amino pada sekuens protein dilakukan pada situs SNAP2. Pemodelan struktur tiga dimensi (3D) Abc1p C. krusei dilakukan di situs SWISS-PROT dan Phyre2. Hasil: Program BLAST menunjukkan protein Abc1p pada spesimen WGS C. krusei dengan panjang antara 1225–1496 asam amino. Ditemukan homolog dari protein Abc1p pada spesimen C. albicans, C. tropicalis, C. parapsilosis, dan C. auris. Program MEGA11 menemukan common ancestor dari protein ini walau beberapa cabang kurang didukung secara statistika. SNAP2 memprediksikan beberapa daerah yang dapat menyebabkan perubahan fungsi protein jika terjadi perubahan asam amino. Pemodelan struktur 3D menemukan bentuk protein yang paling dekat dengan Abc1p C. krusei adalah Pdr5 Saccharomyces cerevisiae. Kesimpulan: Dapat ditemukan hubungan genetik antara protein Abc1p dengan homolognya pada spesimen Candida lain yang juga berperan dalam resistansi Candida tersebut terhadap obat. Hubungan antara protein transpor Abc1p dengan resistansi C. krusei terhadap flukonazol masih belum dapat dijelaskan.
Kata kunci: Candida krusei, Candida spp., bioinformatika, filogeni, protein modeling, resistansi azol



Introduction: Candida is a genus of yeasts that causes candidiasis. This disease has high morbidity and mortality rate, especially for immunocompromised patients. The most common species of Candida that causes candidiasis is C. albicans. In recent times, the number of non-albicans candidiasis (NAC) has been rising. One species that causes NAC is C. krusei. It has a natural resistance to fluconazole. One factor in C. krusei’s resistance against fluconazole is the ATP-binding cassette 1 transport protein (Abc1p) which is coded by the ABC1 gene. Analysis of ABC1 and Abc1p is expected to shed some light towards the resistance mechanism in C. krusei. Method: This study is an experimental observational study to look at the characteristics of the Abc1p protein in sixteen whole-genome sequence specimens of C. krusei from the NCBI genome database. Sequence of the ABC1 gene and Abc1p protein are found by using BLAST with an ABC1 gene from NCBI GeneBank and UniProtKB site as the query. Homologues of the Abc1p protein are found through NCBI protein database using BLAST. Phylogeny analysis of the Abc1p protein and its homologues are determined with MEGA11. Prediciton of effect in amino acid change in the Abc1p sequence is found with SNAP2. The three-dimensional modeling of Abc1p of is done using SWISS-PROT and Phyre2. Result: BLAST result found sequence of Abc1p protein between 1225–1496 amino acid long. Homologues of Abc1p are found in C. albicans, C. tropicalis, C. parapsilosis, and C. auris. Phylogeny analysis found the common ancestor for these proteins even though some branches aren’t statistically supported. SNAP2 predictions found regions in Abc1p with high probability of change in protein function when an amino acid substitution occurs. Protein modeling found Saccharomyces cerevisiae’s Pdr5 protein to be the most structurally similar to Abc1p. Conclusion: Genetic relationship between Abc1p and its homologues in other Candida that plays a role in their resistance towards drugs are found. Correlation between mutation in Abc1p and C. krusei’s resistance against fluconazole can still yet to be explained.
Keywords: Candida krusei, Candida spp., bioinformatics, phylogeny, protein modeling, azole resistance