Rosa Rubicondior: Unintelligent Design - Something Any Intelligent Designer Could Have Done, If It Was Real

The figure depicts the NFR5 kinase structure and juxtamembrane motif

Discovery of a Key Protein Motif Essential for Root Nodule Symbiosis

Scientists at Aarhus University, Denmark, have discovered that barley can be induced to form a symbiotic relationship with nitrogen-fixing bacteria through a simple substitution of two amino acids in a single protein. This tweak enables barley to initiate the same sort of symbiosis that legumes use to “self-fertilise”. They have published their findings in Proceedings of the National Academy of Sciences of the USA.

This is yet another case where we can legitimately ask: if scientists can do it, why didn’t creationism’s supposed intelligent designer do it, if its intent were truly to create a world optimised for human existence? The question remains unanswered, often provoking threats and hysteria on social media, as creationists scramble to cover their confusion with guesses rooted in Christian fundamentalism and Biblical tales of “The Fall”. It’s a core theological patch, while the forlorn Discovery Institute and its fellows remain as silent on this issue as they are on parasites and pathogens—still struggling to sustain the pretence that ID creationism is real science rather than Bible-literalist creationism dressed in a grubby lab coat.

The Aarhus researchers found that a highly conserved protein, present across plant species, plays a crucial role in plant–microbe interactions—presumably as part of the plant’s defence against pathogens. However, in legumes the same protein must be suppressed, because its normal activity prevents formation of the root nodules that act as low-oxygen refuges for the nitrogen-fixing bacteria on which legumes depend. A simple mutation in this protein allows nodule formation in barley, enabling the crop to produce its own nitrogen fertiliser, increasing yields without the expense of artificial fertilisers and without the ecological harm they cause when they leach into waterways.

What Are Nitrogen-Fixing Bacteria?

Cross section of root nodule of pea

Nitrogen-fixing bacteria are microorganisms capable of converting atmospheric nitrogen (N₂) into ammonia (NH₃), a form plants can use to build proteins, nucleic acids, and other essential molecules. Although nitrogen gas makes up about 78% of Earth’s atmosphere, it is chemically inert, so most organisms cannot use it directly.

Where They Live

Root nodules of legumes:
Species such as Rhizobium and Bradyrhizobium infect legume roots and trigger the formation of nodules—specialised low-oxygen compartments where the bacteria can safely fix nitrogen.
Free-living in soil:
Some bacteria, including Azotobacter and Clostridium species, fix nitrogen without a plant partner, although less efficiently.
Associative symbionts:
Certain grasses and cereals host non-nodulating nitrogen-fixers around their roots or between cells, but these associations are generally weak compared with the legume–rhizobium symbiosis.

How Nitrogen Fixation Works

The core enzyme, nitrogenase, reduces atmospheric nitrogen to ammonia. It is highly sensitive to oxygen, which is why nodules maintain a controlled, low-oxygen environment. The plant supplies carbohydrates, while the bacteria supply fixed nitrogen—making it a classic mutualism.

Why It Matters

Natural fertiliser production: Reduces reliance on synthetic nitrogen fertilisers derived from the energy-intensive Haber–Bosch process.
Soil health: Enhances nutrient cycling and improves soil structure.
Agricultural productivity: Legume crops enrich soils for subsequent plantings, lowering input costs.
Environmental benefits: Cuts greenhouse gas emissions and reduces nitrate pollution of waterways.

Why Cereals Don’t Normally Fix Nitrogen

Cereals such as barley, wheat, and maize lack the ability to form nodules. They also possess plant-defence proteins that inhibit the symbiotic signalling pathways needed to establish the partnership. This is why the Aarhus University study—showing that a single protein alteration may permit barley to form these relationships—is scientifically and agriculturally significant.

Their work is summarised in an Aarhus Universität news release by Anne Færch Nielsen.

Discovery of a Key Protein Motif Essential for Root Nodule Symbiosis
Researchers from the Department of Molecular Biology and Genetics at Aarhus University have uncovered a critical structural feature of plant receptors that play a key role in root nodule symbiosis - a process that enables plants to form mutually beneficial relationships with nitrogen-fixing bacteria.
The study, published in PNAS, focuses on the Nod Factor Receptor 5 (NFR5), a plant receptor that recognizes signals from symbiotic bacteria and triggers the formation of nitrogen-fixing nodules on plant roots. NFR5, found in legumes such as Lotus japonicus, is known to partner with NFR1, another receptor protein, to mediate the symbiotic relationship between plants and bacteria. While NFR1’s signaling role depends on its active kinase domain, NFR5 is a pseudokinase without catalytic activity, leaving its role in the symbiotic signaling process unclear - until now.

Simon Hansen in the group of Kasper Røjkjær Andersen has now solved the crystal structure of the intracellular domain of NFR5 and identified a crucial juxtamembrane motif - a hydrophobic region located just inside the cell. This motif, consisting of two α-helices named αA and αA', was found to mediate interactions between individual NFR5 molecules and between NFR5 and NFR1. These interactions are essential for triggering the signaling pathway that leads to nodule formation.

The study's findings reveal that this juxtamembrane motif is highly conserved across various plant species, suggesting that it plays a broader role in plant-microbe interactions beyond legumes. Mutations that disrupt this motif were shown to prevent the formation of root nodules, underlining its importance in symbiosis.

The discovery has implications for agricultural science, particularly in the ongoing efforts to engineer nitrogen-fixing symbiosis into non-legume crops like wheat or corn. By understanding the structural and functional mechanisms of receptors like NFR5, scientists are one step closer to developing crops that can naturally fix nitrogen, potentially reducing the need for synthetic fertilizers and promoting sustainable agriculture. Publication:
S.B. Hansen,T.B. Luu,K. Gysel,D. Lironi,C. Krönauer,H. Rübsam,I.B. Jensen,M. Tsitsikli,T.G. Birkefeldt,A. Trgovcevic,J. Stougaard,S. Radutoiu, & K.R. Andersen
A conserved juxtamembrane motif in plant NFR5 receptors is essential for root nodule symbiosis
Proc. Natl. Acad. Sci. U.S.A. 121 (46) e2405671121, https://doi.org/10.1073/pnas.2405671121 (2024).

Significance
Understanding the molecular mechanisms that enable nitrogen-fixing symbiosis is crucial for ongoing efforts to engineer this trait into nonlegume crops. The plant LysM receptor kinase NFR5 is required for perception of bacterial Nod factor and facilitates signal transduction leading to root nodule symbiosis in legumes. Here, we describe the structure and function of the Lotus NFR5 intracellular part and provide unique insights into the sparsely explored area of pseudokinase biology by identifying a conserved juxtamembrane αA and αA′ motif that mediates protein–protein interaction and is important for the signaling function of NFR5.

Abstract
Establishment of root nodule symbiosis is initiated by the perception of bacterial Nod factor ligands by the plant LysM receptor kinases NFR1 and NFR5. Receptor signaling initiating the symbiotic pathway depends on the kinase activity of NFR1, while the signaling mechanism of the catalytically inactive NFR5 pseudokinase is unknown. Here, we present the crystal structure of the signaling-competent Lotus japonicus NFR5 intracellular domain, comprising the juxtamembrane region and pseudokinase domain. The juxtamembrane region is structurally well defined and forms two α-helices, αA and αA′, which contain an exposed hydrophobic motif. We demonstrate that this “juxtamembrane motif” promotes NFR5–NFR5 and NFR1–NFR5 interactions and is essential for symbiotic signaling. Conservation analysis reveals that the juxtamembrane motif is present throughout NFR5-type receptors and is required for symbiosis signaling from barley RLK10, suggesting a conserved and broader function for this motif in plant–microbe symbioses.

Nod Factor Receptor 5 (NFR5) is required for the perception of rhizobial Nod factors and the subsequent initiation of root nodule symbiosis between legumes and nitrogen-fixing bacteria (1–4). Lotus japonicus (hereafter Lotus) NFR5 contains an extracellular domain of three lysin motifs (LysM), which selectively binds the Nod factor produced by the symbiont of Lotus, Mesorhizobium loti (3, 5–7). NFR5 is embedded in the plant plasma membrane via a single transmembrane helix and intracellularly comprises an N-terminal juxtamembrane region followed by a protein kinase domain and a C-terminal tail (2). The NFR5 kinase domain contains degenerated kinase motifs (e.g., degenerated glycine-rich loop, activation loop, and DFG motif) and is consequently a catalytically inactive pseudokinase (2, 8, 9). In contrast, the receptor partner NFR1 contains a conventional protein kinase domain, and NFR1 phosphorylation activity is required for symbiotic signaling (1, 8). Despite its lack of catalytic activity, the pseudokinase domain of NFR5 is required for establishing root nodule symbiosis, but the molecular mechanism of NFR5 signaling is unknown (10). Kinase phosphorylation signaling is well described in biology, while the signaling mechanisms for catalytically inactive pseudokinases are poorly understood, despite being ubiquitous throughout eukaryotes (11). Generally, receptor kinases form homo- and/or heterocomplexes that are important for their signaling function (12, 13). In Arabidopsis thaliana, these include the leucine-rich repeat (LRR) receptor kinases BRI1, SUB, FLS2, EFR, BIR2, and BAK1 as well as LysM receptor kinases CERK1, LYK4, and LYK5 (14–26). Likewise, an NFR1–NFR5 heterocomplex is required for nodulation in Lotus, while the detailed mechanisms for complex assembly and complex composition are still unclear (4). For receptor pseudokinases, complex formation and signaling have in some cases been linked to conformational toggling of the αC helix, catalytic spine, and regulatory spine that resemble small G-protein signaling, while other pseudokinases mediate protein–protein interactions through flexible regulatory tail regions (27–32). NFR5-type receptors are prevalent throughout plants, and several studies have demonstrated the functional importance of this class of receptors in establishing symbioses between plants and microbes (2, 33–36). Investigating NFR5 complex formation and signaling can inform on how plant receptor kinases work to initiate cellular programs for symbiotic interactions. In this study, we provide insights into NFR5-type receptor signaling mechanisms. We present the crystal structure of the Lotus NFR5 intracellular domain that comprises the core kinase and two juxtamembrane α-helices. We find that NFR5 homo-oligomerizes and that an exposed hydrophobic motif in the juxtamembrane α-helices promotes the assembly of NFR5–NFR5 and NFR1–NFR5 complexes. Our analysis reveals that this motif is conserved throughout NFR5-type receptors and that it is essential for symbiosis signaling in both Lotus NFR5 and barley RLK10.

S.B. Hansen,T.B. Luu,K. Gysel,D. Lironi,C. Krönauer,H. Rübsam,I.B. Jensen,M. Tsitsikli,T.G. Birkefeldt,A. Trgovcevic,J. Stougaard,S. Radutoiu, & K.R. Andersen
A conserved juxtamembrane motif in plant NFR5 receptors is essential for root nodule symbiosis
Proc. Natl. Acad. Sci. U.S.A. 121 (46) e2405671121, https://doi.org/10.1073/pnas.2405671121 (2024).

Copyright: © 2025 The authors.
Published by the National Academy of Science of the USA. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Discoveries like this highlight an awkward truth for creationists: if a small, targeted alteration in a single plant protein can unlock a powerful, yield-boosting symbiosis, then an all-knowing, all-loving designer could have built such a system into cereal crops from the outset. Nothing in the Aarhus team’s work suggests impossibility—only that evolution did not take this particular route in grasses, and that plant defences, shaped by natural selection, came with trade-offs that legumes later circumvented. An omnibenevolent creator would face no such constraints.

Instead, humanity has spent millennia wrestling with nutrient-poor soils, famines, ecological damage from fertilisers, and the high energy cost of industrial nitrogen fixation. A truly benevolent designer could have endowed staple crops like barley, wheat, and rice with the same symbiotic machinery that legumes enjoy, sparing us environmental harm and human suffering on an immense scale. Yet the world we observe is one in which solutions emerge through scientific inquiry, not divine foresight.

So once again, it falls to human curiosity and evidence-based research to repair the flaws and inefficiencies of the natural world. If intelligent design is to be credited anywhere, it belongs with the scientists who uncover these mechanisms and improve them—not with a hypothetical designer whose omissions create the very problems we are left struggling to solve.

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