Characterization of DNA methylation in Malawian Mycobacterium tuberculosis clinical isolates.

Victor Ndhlovu,Benjamin Kumwenda,Wilson Mandala,Konstantina Kontogianni,Mercy Kamdolozi,Marriott Nliwasa,Dean B Everett,Gerry Davies,Derek J Sloan,Mphatso Mwapasa,Maxine Caws,Elizabeth Corbett,Anmol Kiran

doi:10.7717/peerj.10432

Abstract

BackgroundAlthough Mycobacterium tuberculosis (Mtb) strains exhibit genomic homology of >99%, there is considerable variation in the phenotype. The underlying mechanisms of phenotypic heterogeneity in Mtb are not well understood but epigenetic variation is thought to contribute. At present the methylome of Mtb has not been completely characterized.MethodsWe completed methylomes of 18 Mycobacterium tuberculosis (Mtb) clinical isolates from Malawi representing the largest number of Mtb genomes to be completed in a single study using Single Molecule Real Time (SMRT) sequencing to date.ResultsWe replicate and confirm four methylation disrupting mutations in 4 lineages of Mtb. For the first time we report complete loss of methylation courtesy of C758T (S253L) mutation in the MamB gene of Indo-oceanic lineage of Mtb. Additionally, we report a novel missense mutation G454A (G152S) in the MamA gene of the Euro-American lineage which could potentially be attributed to total disruption of methylation in the CCCAG motif but partial loss in a partner motif. Through a genomic and methylome comparative analysis with a global sample of sixteen, we report previously unknown mutations affecting the pks15/1 locus in L6 isolates. We confirm that methylation in Mtb is lineage specific although some unresolved issues still remain.

Highlights

Mycobacterium tuberculosis (Mtb) is the causative agent of Tuberculosis (TB), infecting about 1.7 billion people with 5–10% disease development rate in their lifetime (WHO, 2020)
The Beijing strain is associated with increasing multidrug resistant TB (MDR-TB) (Cowley et al, 2008; Van der Spuy et al, 2009) whereas the East African Indian (EAI) lineage has been associated with lower rates of transmission compared to other lineages (Albanna et al, 2011)
We further report of a novel missense mutation G454A (G152S) in the MamA gene of Euro-American lineage which could potentially be attributed to total disruption of methylation in the CTCCAG motif but partial loss in a partner motif

Summary

Introduction

Mycobacterium tuberculosis (Mtb) is the causative agent of Tuberculosis (TB), infecting about 1.7 billion people with 5–10% disease development rate in their lifetime (WHO, 2020). 10% of the total coding potential contains polymorphic guanine-cytosine repetitive sequences (PGRS) (Cole, 2002; Grover et al, 2018) which encode two unrelated families of acidic glycine-rich proteins- proline-glutamic acid (PE) and proline-proline glutamic acid (PPE) Specific functions of these genes and their proteins remain unclear. At present the methylome of Mtb has not been completely characterized, neither has any resulting information been correlated with phenotypic heterogeneity observed in TB patients. We completed methylomes of 18 Mycobacterium tuberculosis (Mtb) clinical isolates from Malawi representing the largest number of Mtb genomes to be completed in a single study using Single Molecule Real Time (SMRT) sequencing to date. We confirm that methylation in Mtb is lineage specific some unresolved issues still remain

Methods

Results

Conclusion