Rosa Rubicondior: Malevolent Design - The Sneaky Way TB Keeps On Making Us Sick

Study discovers DNA switch that controls TB growth – and could help unlock its antibiotic resistance secrets | University of Surrey

If you're an omniscient, omnipotent, malevolent designer of parasites — such as the bacterium that causes tuberculosis in humans — then you're hardly going to let a little thing like the immune system (which you supposedly also designed to protect them) or even the development of medical science and antibiotics spoil your fun in causing random suffering, are you? Naturally, you'd equip your creation with mechanisms to overcome these obstacles.

Within the framework of Intelligent Design creationism, that's precisely what this recent discovery should look like — at least to those creationists who don't simply ignore the obvious and pretend it isn't there. Scientists from the Universities of Surrey and Oxford have discovered that Mycobacterium tuberculosis uses a reversible process known as ADP-ribosylation to modify its DNA, controlling both replication and gene expression. This allows the bacterium to remain dormant for extended periods and reactivate when environmental threats, such as immune responses or antibiotics, have passed.

This presents a problem for creationists who insist on believing in a benevolent creator deity and simultaneously hold that features such as irreducible complexity and complex specified information are sure signs of intelligent design—claims promoted by Discovery Institute fellows Michael J. Behe and William A. Dembski. Since Mycobacterium tuberculosis displays these very characteristics, so either it was designed specifically to cause suffering, or those characteristics are not the reliable indicators of divine design that Behe and Dembski claim, and their entire argument collapses.

This discovery was recently published open access in The EMBO Journal, and further details are available in the University of Surrey press release:

What information do you have on the origins and pathology of Mycobacterium tuberculosis? Mycobacterium tuberculosis (M. tuberculosis) is the bacterium responsible for tuberculosis (TB), a serious infectious disease that primarily affects the lungs but can also spread to other organs. Here is a detailed overview of its origins and pathology:
Origins and Evolution

Phylogenetic History:
M. tuberculosis belongs to the Mycobacterium tuberculosis complex (MTBC), which includes several closely related species that infect humans and animals (e.g. M. bovis, M. africanum, M. microti). Genetic analysis suggests these species diverged from a common ancestor thousands of years ago.
Co-evolution with Humans:
Genetic and archaeological evidence indicates that M. tuberculosis may have co-evolved with humans for at least 10,000 years, possibly originating in Africa. Some genomic studies propose that it emerged from an environmental mycobacterium that adapted to human hosts, becoming increasingly specialised.
Domestication Hypothesis Refuted:
It was once thought that M. tuberculosis evolved from M. bovis (a cattle pathogen) and jumped to humans with the domestication of animals. However, molecular clock studies have shown that M. tuberculosis likely predates animal domestication and was already a human pathogen before the advent of agriculture.

Pathology and Mechanism of Disease

Transmission: TB spreads via airborne droplets when an infected person coughs, sneezes, or speaks. Only a small number of inhaled bacteria are needed to cause infection in susceptible individuals.
Infection Process:

Initial Infection: The bacteria are inhaled into the lungs and taken up by alveolar macrophages.
Immune Response: Rather than being destroyed, M. tuberculosis can survive and replicate inside macrophages. The immune system responds by forming granulomas, which are clusters of immune cells attempting to contain the infection.
Latency: In many cases, the infection becomes latent, meaning the bacteria are contained but not eliminated. Around a quarter of the world’s population is estimated to carry latent TB.
Reactivation: The bacteria can remain dormant for years and reactivate when the immune system is weakened (e.g. due to HIV, malnutrition, stress, or immunosuppressive therapy), leading to active TB disease.

Clinical Manifestations:

Pulmonary TB: The most common form. Symptoms include persistent cough, chest pain, haemoptysis (coughing up blood), fever, night sweats, fatigue, and weight loss.
Extrapulmonary TB: Can affect lymph nodes, pleura, bones, joints, kidneys, central nervous system, and other organs.

Immune Evasion:

M. tuberculosis has evolved multiple strategies to evade host defences:

Inhibits phagosome-lysosome fusion in macrophages.
Modulates antigen presentation.
Alters host gene expression using mechanisms such as ADP-ribosylation, recently discovered to affect its dormancy and resistance.
Induces necrosis instead of apoptosis in host cells, promoting spread.

Drug Resistance:
The bacterium can develop resistance to antibiotics, notably isoniazid and rifampicin, resulting in multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB). Resistance arises through mutations and selective pressure from incomplete or improper treatment.

Public Health Impact

TB remains one of the top infectious killers globally:

According to the WHO (2023), over 10 million people fall ill with TB each year, and more than 1.3 million die from it.
TB is especially deadly in people with HIV, due to weakened immunity.
It is a disease of poverty, strongly associated with overcrowded living conditions, undernutrition, and poor access to healthcare.

Study discovers DNA switch that controls TB growth – and could help unlock its antibiotic resistance secrets
The bacteria that cause tuberculosis (TB) may have an “on-off switch” that lets them pause and restart growth, according to a new study from the University of Surrey and the University of Oxford. The research helps explain why TB is so hard to treat with antibiotics and could pave the way for better drugs.

We’ve found a way that Mycobacterium tuberculosis can slow down its growth and potentially allow it to hide from the immune response and resist antibiotics. By showing that ADP-ribosylation of DNA can control both replication and gene expression, we’ve discovered a new layer of regulation that could be key to understanding TB’s persistence. If we can target this process, we could make the bacteria easier to eliminate – especially in the slow-growing or dormant states that current treatments struggle to reach.

Professor Graham Stewart, corresponding author
Section of Bacteriology
School of Biosciences
University of Surrey, Guildford, Surrey UK.

The study focused on two enzymes: DarT, which adds the ADP-ribose tag to DNA, and DarG, which removes it. When DarT is active, it stops the bacteria from copying their DNA and dividing. When DarG removes the tag, growth resumes. This start-and-stop control may help the bacteria survive in harsh conditions, making them more resilient during long-term infections.

To find out more about how this molecular switch works, the researchers used a CRISPR interference (CRISPRi) system to selectively reduce levels of DarG. This allowed DarT to act without restraint, leading to the build-up of DNA modifications and halting bacterial growth. The team then used a technique called ADPr-Seq to map where these tags appeared across the genome, alongside live-cell imaging and RNA sequencing to track changes in DNA replication, cell division and gene expression. These tools helped reveal how ADP-ribosylation affects both the ability of the bacteria to replicate and the activity of genes needed for survival in stressful environments.

According to the World Health Organization, TB kills 1.25 million people globally every year. In 2023, around 10.8 million people fell ill with the disease.

Abstract
Mycobacterium tuberculosis maintains long-term infections characterised by the need to regulate growth and adapt to contrasting in vivo environments. Here we show that M. tuberculosis complex bacteria utilise reversible ADP-ribosylation of single-stranded DNA as a mechanism to coordinate stationary phase growth with transcriptional adaptation. The DNA modification is controlled by DarT, an ADP-ribosyltransferase, which adds ADP-ribose to thymidine, and DarG, which enzymatically removes this base modification. Using darG-knockdown M. bovis BCG, we map the first DNA ADP-ribosylome from any organism. We show that inhibition of replication by DarT is reversible and accompanied by extensive ADP-ribosylation at the origin of replication (OriC). In addition, we observe ADP-ribosylation across the genome and demonstrate that ADP-ribose-thymidine alters the transcriptional activity of M. tuberculosis RNA polymerase. Furthermore, we demonstrate that during stationary phase, DarT-dependent ADP-ribosylation of M. tuberculosis DNA is required to optimally induce expression of the Zur regulon, including the ESX-3 secretion system and multiple alternative ribosome proteins. Thus, ADP-ribosylation of DNA can provide a mechanistic link through every aspect of DNA biology from replication to transcription to translation.

Synopsis

Mycobacterium tuberculosis causes long-term infections characterised by slow or non-replicating growth states and controlled gene expression. This study finds these bacteria as the first example of an organism using ADP-ribose modification of DNA as a mechanism for regulating gene transcription and cellular replication.

The DNA-ADP-ribosylome can be mapped across the genome by ADPr-Seq.
ADP-ribosylation of thymidine by DarT-DarG in M. tuberculosis provides a dynamically flexible DNA switch.
ADP-ribosylation at the origin of chromosomal replication (OriC) controls replication.
ADP-ribosylation of promoter DNA regulates transcription of genes in stationary growth phase, including alternative ribosome subunits and the ESX-3 Type 7 Secretion System.

Introduction
Mycobacterium tuberculosis is the leading single cause of death by an infectious disease, killing 1.25 million people in 2023 (WHO, 2024). New antibiotics have recently been added to the multidrug panels that constitute the backbone of tuberculosis (TB) treatment. Yet, M. tuberculosis still presents a frustrating recalcitrance to drug therapy, with treatment regimens typically lasting from 4 to 6 months even for fully drug-sensitive infections (WHO, 2022). Perhaps the biggest reason for this persistence in the face of efficacious drugs is the presence of subpopulations of mycobacteria which replicate slowly or not at all and are tolerant to drugs. In addition, a significant proportion of infected individuals carry a latent asymptomatic infection of putatively non-replicating mycobacteria, which can re-activate, perhaps years later, sustaining transmission. Indeed, the ability to tightly regulate replication and grow slowly may be an important trait for pathogenic bacteria in general (Leggett et al, 2017) and mycobacteria in particular.

ADP-ribosylation is a well-established posttranslational modification of proteins, but recently it became apparent that reversible ADP-ribosylation of nucleic acids is widespread (Groslambert et al, 2021; Suskiewicz et al, 2023). Previously, we defined the molecular mechanisms of an ADP-ribosyltransferase, DarT2 (hereon known as DarT), which catalyses DNA base modification by adding an ADP-ribose to the in-ring N3 of thymine in single-stranded DNA (ssDNA) (Schuller et al, 2021.1). In M. tuberculosis, DarT is co-expressed with the macrodomain-containing DarG protein, a DNA ADP-ribosylglycohydrolase, which regulates DarT activity by enzymatic removal of ADP-ribose from modified thymine in addition to direct antagonistic physical interaction with DarT (Deep et al, 2023.1; Jankevicius et al, 2016; Schuller et al, 2021.1).

DarT is present in many bacteria and, in some, an orthologous system, DarT1, is also present, catalysing ADP-ribosylation of guanosine bases in ssDNA (Cihlova et al, 2024.1; Schuller et al, 2023.2). In most bacteria, these systems appear to function in phage defence (LeRoux et al, 2022.1), however, the potential utility of reversible DNA modification raised the question of whether these enzyme systems may also provide mechanisms for regulation of DNA biology and cellular function. To answer this question, we chose to examine M. tuberculosis because DarT-DarG was ubiquitous in all members of the pathogenic M. tuberculosis Complex and was genomically situated in a transcriptional unit with the replicative helicase DnaB rather than in a phage defence island. We previously demonstrated that unregulated DarT activity was massively toxic to bacterial cells but the DarT-DarG module in M. tuberculosis regulated growth by ADP-ribosylation of the origin of chromosome replication (Schuller et al, 2021.1).

To investigate further the role of DarT-DarG in gene and chromosome regulation, here we examined the phenotypic effects of DarT-DarG activity on replication and investigated whether ADP-ribosylation of the mycobacterial genome provides a dynamically flexible switch. We utilised affinity-sequencing to identify ADP-ribosylation sites across the genome and explored how ADP-ribosylation of thymidine affects the initiation, regulation and progression of transcription, providing for the first time in any organism evidence that modification of a DNA base with ADP-ribose provides a mechanism to coordinate DNA replication with transcriptional adaptation.

Butler, Rachel E; Schuller, Marion; Jaiswal, Ritu; Mukhopadhyay, Jayanta; Barber, Jim; Hingley-Wilson, Suzie; Wasson, Emily; Couto Alves, Alex; Ahel, Ivan; Stewart, Graham R
Control of replication and gene expression by ADP-ribosylation of DNA in Mycobacterium tuberculosis
The EMBO Journal (2025) 1-24, DOI: 10.1038/s44318-025-00451-y

Copyright: © 2025 The authors.
Published by John Wiley & Sons, Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

The existence and behaviour of Mycobacterium tuberculosis pose a serious challenge to creationist claims of an all-loving, intelligent designer. This bacterium not only causes immense human suffering and death, but has also evolved highly sophisticated mechanisms—such as the recently discovered DNA-modifying process ADP-ribosylation—that allow it to evade the immune system, survive antibiotics, and lie dormant for years.

If, as proponents of Intelligent Design argue, such complex mechanisms are the product of purposeful design, then one must conclude that M. tuberculosis was deliberately engineered to persist, spread, and cause disease. This is profoundly at odds with the idea of a benevolent creator. Alternatively, if these harmful traits are not the result of intelligent design, then the central claims of ID—such as irreducible complexity and complex specified information—fail to explain biological complexity consistently.

Either way, M. tuberculosis exposes a fatal contradiction in creationist reasoning.

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