Mycobacterium tuberculosis ESAT-6 Protein Undergoes pH-Dependent Self-Association and an ESAT-6-Specific Nanobody Restricts Intracellular Bacterial Growth

Core Concepts

The ESAT-6 protein from Mycobacterium tuberculosis undergoes rapid self-association into large complexes at acidic pH levels, which may be preceded by the formation of stable tetramers. An ESAT-6-specific nanobody, E11rv, can inhibit the growth of M. tuberculosis inside host cells.

Abstract

This study investigates the biochemical properties and functional significance of the ESAT-6 protein from Mycobacterium tuberculosis (Mtb), a key virulence factor that enables the bacteria to disrupt the phagosomal membrane and survive within host macrophages.
The key findings are:

ESAT-6 exists as a homodimer at neutral pH, but undergoes rapid self-association into large complexes at acidic pH levels below 5.0. This self-association may be preceded by the formation of stable ESAT-6 tetramers.

The tight binding between ESAT-6 and its chaperone protein CFP-10 is maintained even at acidic pH, suggesting that ESAT-6 self-association and membrane disruption may occur independently of CFP-10 dissociation.

Molecular modeling indicates that ESAT-6 self-association likely involves interactions between both the hydrophobic and hydrophilic faces of the protein, stabilized by salt bridges.

The authors generated an ESAT-6-specific alpaca-derived nanobody, E11rv, which binds to ESAT-6 with high affinity. Treating Mtb-infected macrophages with E11rv or expressing E11rv in the host cell cytoplasm significantly inhibited the growth of intracellular Mtb.

These findings provide important insights into the pH-dependent self-association behavior of ESAT-6 and demonstrate the potential of ESAT-6-targeting molecules like E11rv as novel therapeutic approaches against tuberculosis.

Stats

ESAT-6 and CFP-10 form a tight 1:1 complex with a dissociation constant (KD) of 220 pM at neutral pH.
ESAT-6 self-associates into large complexes at acidic pH, with an apparent KD of ~1.5 μM.
The ESAT-6-specific nanobody E11rv binds to ESAT-6 with a KD of 331-376 nM.
Treating Mtb-infected macrophages with E11rv or expressing E11rv in the host cell cytoplasm significantly inhibited intracellular Mtb growth.

Quotes

"ESAT-6 undergoes rapid self-association into large complexes under acidic conditions, leading to the identification of a stable tetrameric ESAT-6 species."
"We show that cytoplasmic expression of an anti-ESAT-6 nanobody blocks Mtb replication, thereby underlining the pivotal role of ESAT-6 in intracellular survival."

Key Insights Distilled From

ESAT-6 undergoes self-association at phagosomal pH and an ESAT-6 specific nanobody restricts M. tuberculosis growth in macrophages

by Bates,T. A.,... at www.biorxiv.org 08-17-2023

https://www.biorxiv.org/content/10.1101/2023.08.16.553641v3

Deeper Inquiries

How might the pH-dependent self-association of ESAT-6 be regulated or modulated by other Mtb factors to control its membrane disruption activity?

The pH-dependent self-association of ESAT-6 could be regulated or modulated by other Mtb factors through several mechanisms. One possibility is that other proteins or factors within the Mtb cell could interact with ESAT-6 and influence its self-association behavior. These interactions could stabilize or destabilize ESAT-6 complexes, impacting its ability to disrupt membranes. Additionally, post-translational modifications of ESAT-6 or other regulatory proteins could alter the pH sensitivity of ESAT-6 self-association. For example, phosphorylation or acetylation of ESAT-6 or interacting proteins could modulate the pH-dependent conformational changes that drive self-association. Furthermore, Mtb may have specific chaperones or accessory proteins that assist in regulating the pH-dependent behavior of ESAT-6. These chaperones could facilitate ESAT-6 folding or oligomerization in a pH-dependent manner, fine-tuning its membrane disruption activity.

What are the potential mechanisms by which the ESAT-6-specific nanobody E11rv inhibits Mtb growth inside host cells, beyond simply binding and sequestering ESAT-6?

The ESAT-6-specific nanobody E11rv may inhibit Mtb growth inside host cells through various mechanisms beyond simple binding and sequestering of ESAT-6. One potential mechanism is the interference with ESAT-6's interaction with host cell factors critical for Mtb survival and replication. By binding to ESAT-6, E11rv could disrupt ESAT-6's ability to interact with host cell proteins or membranes, thereby interfering with essential processes for Mtb intracellular survival. Additionally, E11rv binding to ESAT-6 may trigger immune responses or signaling pathways within the host cell that lead to the inhibition of Mtb growth. This could involve the activation of immune cells or pathways that target and eliminate Mtb-infected cells. Moreover, E11rv binding to ESAT-6 could induce conformational changes in ESAT-6 that render it non-functional or target it for degradation within the host cell. By altering the structure or stability of ESAT-6, E11rv may effectively neutralize its membrane disruption activity and hinder Mtb replication.

Could the insights into ESAT-6 structure and self-association behavior be leveraged to develop small molecule inhibitors that disrupt ESAT-6 function and Mtb intracellular survival?

The insights gained from studying ESAT-6 structure and self-association behavior could indeed be valuable for the development of small molecule inhibitors that target ESAT-6 function and inhibit Mtb intracellular survival. By understanding the specific regions of ESAT-6 involved in self-association and membrane disruption, researchers can design small molecules that target these critical sites and interfere with ESAT-6 activity. For example, compounds that disrupt the hydrophobic or hydrophilic interfaces involved in ESAT-6 self-association could prevent the formation of large ESAT-6 complexes and inhibit its membrane-disrupting capabilities. Additionally, small molecules that stabilize ESAT-6 in an inactive conformation or promote its degradation could effectively neutralize its virulence. Furthermore, targeting the pH-dependent nature of ESAT-6 self-association with specific inhibitors could provide a strategy to modulate its activity within the acidic phagosomal environment. Overall, leveraging the structural insights into ESAT-6 to design small molecule inhibitors holds promise for developing novel therapeutics that target ESAT-6 and combat Mtb intracellular survival.