Lineage-Specific Proteomic Signatures in the Mycobacterium tuberculosis Complex Reveal Differential Abundance of Proteins Involved in Virulence, DNA Repair, CRISPR-Cas, Bioenergetics and Lipid Metabolism.

Solomon Abebe Yimer,Timo Lutter,Carol Holm-Hansen,Alemayehu Godana Birhanu,Tone Tønjum,Håvard Homberset,Abraham Aseffa,Ephrem Debebe Zegeye,Shewit Kalayou,Tahira Riaz,Markos Abebe

doi:10.3389/fmicb.2020.550760

Abstract

Despite the discovery of the tubercle bacillus more than 130 years ago, its physiology and the mechanisms of virulence are still not fully understood. A comprehensive analysis of the proteomes of members of the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages 3, 4, 5, and 7 was conducted to better understand the evolution of virulence and other physiological characteristics. Unique and shared proteomic signatures in these modern, pre-modern and ancient MTBC lineages, as deduced from quantitative bioinformatics analyses of high-resolution mass spectrometry data, were delineated. The main proteomic findings were verified by using immunoblotting. In addition, analysis of multiple genome alignment of members of the same lineages was performed. Label-free peptide quantification of whole cells from MTBC lineages 3, 4, 5, and 7 yielded a total of 38,346 unique peptides derived from 3092 proteins, representing 77% coverage of the predicted proteome. MTBC lineage-specific differential expression was observed for 539 proteins. Lineage 7 exhibited a markedly reduced abundance of proteins involved in DNA repair, type VII ESX-3 and ESX-1 secretion systems, lipid metabolism and inorganic phosphate uptake, and an increased abundance of proteins involved in alternative pathways of the TCA cycle and the CRISPR-Cas system as compared to the other lineages. Lineages 3 and 4 exhibited a higher abundance of proteins involved in virulence, DNA repair, drug resistance and other metabolic pathways. The high throughput analysis of the MTBC proteome by super-resolution mass spectrometry provided an insight into the differential expression of proteins between MTBC lineages 3, 4, 5, and 7 that may explain the slow growth and reduced virulence, metabolic flexibility, and the ability to survive under adverse growth conditions of lineage 7.

Highlights

Despite the discovery of Mycobacterium tuberculosis (Mtb) more than 130 years ago, Mtb physiology and the mechanisms of virulence are still not fully understood
This study presents novel findings regarding differential protein abundance/protein expression in Mtb lineage 7 versus the other clinically relevant Mycobacterium tuberculosis complex (MTBC) lineages 3, 4, and 5
The reduced abundance of proteins involved in type VII ESX-3 and ESX1 secretion systems, TCA cycle and oxidative phosphorylation, lipid metabolism and DNA repair in lineage 7 may contribute to the slow growth and less virulent phenotype, which corroborates a previous report (Yimer et al, 2017)

Summary

Introduction

Despite the discovery of Mycobacterium tuberculosis (Mtb) more than 130 years ago, Mtb physiology and the mechanisms of virulence are still not fully understood. More than 10.4 million individuals develop active tuberculosis (TB) globally every year, causing 1.3 million deaths annually (World Health Organization [WHO], 2019). The high morbidity and mortality associated with disease caused by Mtb reflects challenges in detecting and diagnosing TB at early stages, as well as poor therapeutic options. A better understanding of the biology of Mtb may expedite the development of the new and innovative tools in demand. Mtb is a facultative intracellular organism that can adapt to the human host and exerts virulence and immune surveillance (Barth et al, 2013). A better understanding of the mechanisms by Mtb evades the host defense system may contribute to the development of novel therapeutics for TB

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