Malevolent Design - How Bacteria Are 'Designed' With a Protective Coat

Bacterial cell wall structure

AI generated (ChatGPT40)
With apologies for the spelling!

Study unveals a novel protective mechanism in bacterial cell wall

Structure of gram-negative cell envelope

By Jeff Dahl - Own work, CC BY-SA 4.0, Link

Here's a conundrum for creationists who have fallen for the Deception Institute's biologically nonsensical excuse for parasites - that they weren't designed by the only entity capable of designing living organisms, but by a process of 'devolution' [sic] from an initial created perfection caused by 'genetic entropy'. This excuse was hastily cobbled together by Michael J Behe when he realised his 'intelligent [sic] design' notion was making creationism's putative creator look like a pestilential malevolence, especially after Behe had gone to such lengths and scuppered his academic credentials with how 'irreducibly-complex-therefore-magically-created' E. coli flagellum, then his claim that resistance to antimalarial drugs in Plasmodium falciparum must have been designed.

The problem was that having produced an excuse for parasites that was designed to appeal to religious fundamentalists, Behe inadvertently abandoned any pretense that creationism is science not religion, by incorporating Christian fundamentalism in his excuse - initial created perfection followed by 'genetic entropy' caused by 'Sin', which depends on a belief in 'The Fall' and original sin.

Although Behe insists he's not a Christian fundamentalist YEC, his books invariably appeal to, and reinforce the prejudices of, those who are, and feed their insatiable demand for validation from the science they despise and continually attack as biased/Satanic/lies/flawed, etc.

But now we have research that shows how bacteria are 'designed' with a protective cell wall which helps them resist enzymes which would otherwise destroy them. Defensive structures and processes cannot logically be described as 'devolutionary', they therefore either evolved naturally, or, if you reject evolution in favour of intelligent [sic] design, were intelligently designed to make the bacteria better at making us sick, i.e., with malevolent intent.

Tell me about the structure of bacterial cell walls, please. Bacterial cell walls are critical to the structure, protection, and shape of bacterial cells. They are primarily composed of a molecule called peptidoglycan, a polymer made of sugars and amino acids that form a mesh-like structure around the cell membrane.

Structure:

• Peptidoglycan Layer: This is the main structural component, providing rigidity. It consists of repeating disaccharide units of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). These sugar chains are cross-linked by short peptide chains, creating a strong, protective mesh.
• Gram-Positive Bacteria:
  • Thick peptidoglycan layer (20-40 nm).
  • Contain teichoic acids and lipoteichoic acids that help maintain the cell wall's rigidity and are involved in cell wall synthesis.
• Gram-Negative Bacteria:
  • Thin peptidoglycan layer (2-7 nm).
  • Surrounded by an outer membrane containing lipopolysaccharides (LPS), which play a role in immune response and provide extra protection.
  • Periplasmic space: The area between the inner membrane and the outer membrane that houses enzymes and other proteins.
• Other Components: Some bacteria have additional layers like capsules or S-layers that provide further protection or adhesion abilities.

What is the significance of gram-negative and gram-positive in the context of bacterial classification?

The distinction between gram-positive and gram-negative bacteria is a fundamental classification based on their cell wall structure and their response to the Gram stain, a laboratory technique developed by Hans Christian Gram in 1884.

Significance in Bacterial Classification:

1. Cell Wall Structure:
   • Gram-Positive Bacteria:
     • Have a thick peptidoglycan layer (20-40 nm), which retains the crystal violet stain used in Gram staining, making these cells appear purple under a microscope.
     • Contain teichoic acids and lipoteichoic acids that are involved in maintaining the cell wall's structure and regulating ion movement.
     • Lack an outer membrane, making them generally more susceptible to antibiotics like penicillin, which target peptidoglycan synthesis.
2. Gram-Negative Bacteria:
   • Have a thin peptidoglycan layer (2-7 nm) located between an inner membrane and an outer membrane. The outer membrane contains lipopolysaccharides (LPS), which are critical for the bacteria's defense and interaction with the host.
   • During Gram staining, they lose the crystal violet stain and take up the counterstain (safranin), appearing pink or red.
   • The outer membrane provides extra protection, making them more resistant to many antibiotics, disinfectants, and the host's immune responses.
   
   
3. Medical Relevance:
   • Gram-positive bacteria include pathogens like Staphylococcus aureus and Streptococcus pneumoniae, responsible for infections like pneumonia, sepsis, and skin infections.
   • Gram-negative bacteria include notorious pathogens like Escherichia coli, Salmonella, and Pseudomonas aeruginosa. These bacteria are often associated with drug resistance because of their impermeable outer membrane and the presence of efflux pumps that expel antibiotics.
   • The lipopolysaccharides (LPS) in gram-negative bacteria can trigger strong immune responses, leading to conditions like septic shock.
4. Antibiotic Sensitivity:
   • Gram-positive bacteria are generally more vulnerable to antibiotics that target the thick peptidoglycan layer, like beta-lactams (e.g., penicillin, cephalosporins) and vancomycin.
   • Gram-negative bacteria are more resistant to such antibiotics due to the outer membrane barrier. Treatments often require antibiotics that can penetrate or disrupt the outer membrane, such as polymyxins, aminoglycosides, or broad-spectrum cephalosporins.
5. Gram-Negative Outer Membrane & Endotoxins:
   • The outer membrane of gram-negative bacteria contains endotoxins (part of the LPS) that can cause inflammation and fever in humans. These endotoxins are released when the bacteria die, which can lead to septic shock if large amounts are released.
6. Gram Staining as a Diagnostic Tool:
   • Gram staining is one of the first steps in the identification and classification of bacteria in clinical microbiology. By observing the color under a microscope, medical professionals can quickly determine whether an infection is caused by a gram-positive or gram-negative organism, guiding the choice of antibiotic treatment.

Summary of Key Differences:

• Gram-Positive Bacteria:
  • Peptidoglycan Layer: Thick (20-40 nm)
  • Teichoic Acids: Present
  • Outer Membrane: Absent
  • Gram Staining: Purple (retains crystal violet)
  • Antibiotic Sensitivity: More sensitive to beta-lactams
  • Endotoxins (LPS): Absent
• Gram-Negative Bacteria:
  • Peptidoglycan Layer: Thin (2-7 nm)
  • Teichoic Acids: Absent
  • Outer Membrane: Present
  • Gram Staining: Pink or red (safranin stain)
  • Antibiotic Sensitivity: More sensitive to beta-lactams
  • Endotoxins (LPS): Present (can cause septic shock)

In summary, the gram-positive and gram-negative distinction provides critical insight into the structural, biochemical, and medical properties of bacteria. This helps in diagnosing bacterial infections, selecting appropriate antibiotics, and understanding bacterial resistance.

Like Behe's 'irreducibly-complex-therefore-intelligently-designed' bacterial flagellum, a defensive cell wall can't be described as the result of 'devolution' from something worse without stretching the meaning of 'perfection' beyond breaking point. Without wishing to state the obvious, a bacterium without a defensive cell wall is less perfect than one with a defensive cell wall. This is how evolution works!

The team which discovered the mechanism that protects bacteria was led by researchers from Umeå University, Sweden, with colleagues from Cornell University, USA. They have just published their findings open access in the journal Nature and announced it in an Umeå University news release:

Study unveals a novel protective mechanism in bacterial cell wall

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Researchers from Umeå University, Sweden, and Cornell University, USA, have discovered a widespread mechanism in bacteria that enhances the bacteria's defense against environmental threats. The discovery, which may be important for research into developing new treatments, shows how a specific crosslinking mode in the peptidoglycan cell wall inhibits the activity of certain cell wall degrading enzymes, and thus protects the bacteria.

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Bacteria are protected by the peptidoglycan cell wall, which helps them withstand internal turgor pressure and external damages such as such as attacks from other bacteria and viruses. To grow and stay strong, bacteria need a balance of enzymes that build up and break down the cell wall. An important type of enzyme that break down the peptidoglycan chains are the lytic transglycolases. However, the regulatory mechanisms governing them have remained elusive until now.

The study, led by Felipe Cava's laboratory at Umeå University in collaboration with colleagues at Cornell University in New York, reveals that a specific type of crosslinking in the cell wall, known as LD-crosslinking, inhibits the activity of the lytic transglycolases.

This has major biological consequences. For example, some bacteria use this type of enzymes to release cell wall fragments that modulate the host immune system. Some bacteria and viruses also use this type of enzymes to kill other bacteria. By controlling the activity of these enzymes, bacteria can potentially protect themselves from the immune system and attacks from other bacteria and viruses.

The discovery fills an important gap in the understanding the role of LD-crosslinking in cell wall homeostasis. We have shown that bacteria can improve their protection against environmental threats, including phage attacks, through a single structural modification in their cell wall.

Professor Felipe Cava, lead author
Department of Molecular Biology
Umeå University, Umeå, Sweden.

The discovery provides new insights into bacterial cell wall homeostasis and opens potential avenues for developing novel antibacterial therapies.

By targeting LD-crosslinking, new treatments could be designed to weaken bacteria's defenses, making them more vulnerable to antibiotics and immune responses.

Laura Alvarez, co-first author
Department of Molecular Biology
Umeå University, Umeå, Sweden.

The study, which is published in the scientific journal Nature Communications, is funded by the Swedish Research Council, the Knut and Alice Wallenberg Foundation and the Kempe Foundations.

Felipe Cava is Professor of Infection Biology, Department of Molecular Biology, Umeå University and affiliated senior group leader with the Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR) and the Integrated Science Lab (Icelab) and SciLifeLab.

About the study:

Control of bacterial cell wall autolysins by peptidoglycan crosslinking mode.
Laura Alvarez, Sara B. Hernandez, Gabriel Torrens, Anna I. Weaver, Tobias Dörr & Felipe Cava.
Nature Communications (2024) DOI https://doi.org/10.1038/s41467-024-52325-2
https://www.nature.com/articles/s41467-024-52325-2

I'll include the technical details from the team's paper in Nature so creationists can thrill at the brilliance of their putative divine malevolence or alternatively point of the results of 'genetic entropy' and 'devolution':

Abstract
To withstand their internal turgor pressure and external threats, most bacteria have a protective peptidoglycan (PG) cell wall. The growth of this PG polymer relies on autolysins, enzymes that create space within the structure. Despite extensive research, the regulatory mechanisms governing these PG-degrading enzymes remain poorly understood. Here, we unveil a novel and widespread control mechanism of lytic transglycosylases (LTs), a type of autolysin responsible for breaking down PG glycan chains. Specifically, we show that LD-crosslinks within the PG sacculus act as an inhibitor of LT activity. Moreover, we demonstrate that this regulation controls the release of immunogenic PG fragments and provides resistance against predatory LTs of both bacterial and viral origin. Our findings address a critical gap in understanding the physiological role of the LD-crosslinking mode in PG homeostasis, highlighting how bacteria can enhance their resilience against environmental threats, including phage attacks, through a single structural PG modification.

Introduction
Bacteria are almost universally encased by a cell wall that is essential for their structural integrity. The main component of the cell wall is the peptidoglycan (PG), also known as murein, a net-like heteropolymer of glycan strands composed of repeats of the disaccharide N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), crosslinked by short peptides¹. Because the so-called PG sacculus envelopes the cytoplasmic membrane and alters the interface with the surroundings, its chemical structure must be dynamically altered during growth and in response to the environmental changes^2,3.

Growth of PG relies on the coordinated action of synthetic and degradative enzymes. Synthetic enzymes include transglycosylases and transpeptidases, which polymerize and crosslink PG chains, respectively⁴. Among these, PG crosslinking is primarily mediated by Penicillin Binding Proteins (PBPs). However, in many bacteria, there are alternative transpeptidases known as LD-transpeptidases (LDTs)⁵. A key distinction between these two types of crosslinks lies in the mechanisms of their formation: PBPs form new peptide bonds connecting the fourth D-Ala of the donor muropeptide and the D-chiral center of the diamino acid in the third position of an adjacent acceptor muropeptide, resulting in a 4,3- or DD-crosslink, while LDTs connect the L- and D-stereocenters of two adjacent diamino acid residues, generating a 3,3- or LD-crosslink⁵. Both crosslink types serve to strengthen the cell wall^6,7. However, LDTs have the unique ability to form linkages not only within PG but also between PG and outer membrane proteins^8,9,10. Although LDTs are not typically essential for bacterial survival, they play significant roles in various processes, including incorporation of non-canonical D-amino acids into PG^2,11, beta-lactam resistance^12,13,14,15 and preservation of cell envelope integrity during failure of LPS translocation¹³. Despite these known roles, the overall physiological function of LDTs remains unclear⁵.

PG degrading enzymes, known as autolysins, cleave covalent bonds within the existing sacculus, enabling the insertion of newly synthesized material. However, these activities can be a double-edged sword: while indispensable for bacterial growth, they need to be carefully controlled to prevent cell lysis^16,17.

The extent to which various classes of autolysins contribute to the expansion of the sacculus, cell division, and overall vegetative growth, as well as the mechanisms and regulatory processes involved, are subject of ongoing research. Autolysins are categorized based on the specific bonds they target within PG and are further differentiated by their unique catalytic domains^17,18. Endopeptidases break the internal bonds, including crosslinks, within the peptide stem, while carboxypeptidases cut the terminal bonds. Amidases split the amide bond that connects the glycan strand to the stem peptide, specifically between MurNAc and L-alanine residues. Glycosidases, such as lysozyme or lytic transglycosylases (LTs), target the glycan strands themselves.

Lysozymes, also known as N-acetylmuramidases or muramidases, and LTs both act on the same β−1,4-glycosidic bond, albeit through distinct mechanisms. Lysozymes hydrolyze this bond, resulting in a product with a non-cyclic terminal reducing MurNAc residue. In contrast, LTs, which are not hydrolases, cleave the bond between MurNAc and GlcNAc, leading to the formation of anhydro-MurNAc capped products, also known as anhydromuropeptides^19,20. LTs are broadly conserved in bacteria and can be categorized as exolytic if they attack glycosidic bonds located at the termini of the glycan chains and release soluble anhydromuropeptides, or endolytic if they cleave non-terminal bonds within the glycan chain^21,22.

LT enzymes are generally implicated in cell growth and division^23,24,25 and in the assembly of transenvelope complexes such as the type VI secretion system²⁶. They are also involved in the release of extracellular PG fragments that serve as signals in adaptive responses such as beta-lactam resistance, and in bacteria-host interactions^27,28. Although the structural and biochemical properties of LTs have been extensively studied, their regulation remains poorly understood.

Here, we used Vibrio cholerae as a Gram-negative model organism to study the changes that PG undergoes amidst environmental shifts. Our research has uncovered a widespread control mechanism: LD-crosslinks within the PG sacculus serve as inhibitors of the activity of LTs. PG analysis under different conditions alongside the use of ldt mutants that, while lacking LD-crosslinks, maintain the total crosslinking stable due to an increase in DD-crosslinks, underscored the superior inhibitory influence of LD-crosslinks compared to DD-crosslinks on the activity of LTs. Through various in vitro and in vivo approaches, we established that this structural interference selectively impacts LTs, while sparing lysozymes. We also discerned that the degree of LD-crosslinking is instrumental in regulating the dispersal of immunogenic PG fragments and provides a defense mechanism against LTs originating from both bacterial and viral origins. The observed fluctuations in LD-crosslinking under various conditions suggest that this mode of crosslinking is modulated by environmental factors, rather than being a direct countermeasure to LT-induced stress. This discovery highlights the physiological importance of LD-crosslinking in PG homeostasis and illustrates how bacteria can enhance their defenses against ecological menaces, such as phage incursions, by modulating their PG crosslinking strategy.

Alvarez, L., Hernandez, S.B., Torrens, G. et al.
Control of bacterial cell wall autolysins by peptidoglycan crosslinking mode. Nat Commun 15, 7937 (2024). https://doi.org/10.1038/s41467-024-52325-2

Copyright: © [year] The authors.
Published by [publisher]. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

I invite any creationists to point out where in that description of the bacterial cell wall, and in particular how it is 'designed' to minimise damage and so preserve the contents, the process that produced it can be described as devolutionary or due to genetic entropy.

If not, which part should be attributed to a divine creator; or should it all be attributed to a natural, god-free, mindless process identical in all respects to evolution?

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