Left three images: close-ups of tomato trichomes where acylsugars are produced. These sticky chemicals act as natural flypaper for potential pests. On the right: a close-up of tomato plant roots covered in small hairs.
Credit: Rachel Kerwin
Creationism's intelligent [sic] designer, unlike a normal intelligent designer worthy of the name, seems to have a moto:
However, even for someone familiar with all the different ways creationism's putative designer has designed for doing the same thing - flight, swimming, body-plan, respiratory systems and eyes, to name but a few - and the regularity with which its 'designs' turn out to be the opposite of what an intelligent designer would design, it will come as no surprise that it has managed to surpass itself with the design of two different metabolic pathways for doing the same thing in the same plant!
Scientists at Michigan State University, Robert Last, have discovered that tomato plant roots produce defensive sugars - acylsugars - by two different metabolic pathways.
And, as an added embarrassment for the creation cult, they have shown that these two pathways came about as a result of new genetic information arising by accidental gene duplication almost 17 million years before they believe Earth existed.
Acylsugars are a class of very sticky sugars produced in specialized cells in the tip of the tricomes of plants of the tomato (Solanaceae) family, which includes aubergines, potatoes, nightshades, peppers and tobacco. Their purpose appears to be to act as a sort of natural flypaper. However, they are also found in the roots of tomato plants, but the root acylsugars are different enough from the tricome acylsugars to almost warrant a separate class of sugars.
It was while investigating the reason for this difference that the Michigan State University team discovered what they termed a 'parallel universe' of metabolic pathways and the genes that control them. They discovered that if you knock out the genes for making root acylsugars, this doesn't affect their production in the tricomes and if you knock out the genes that control the tricome production, acysugars are still produced in the roots.
The team’s findings are the subject of an open access paper published recently in Science Advances. They also explain the background to the study in a Michigan State University news release:
Looking at public genetic sequence data, Kerwin noticed that many of the genes expressed in tomato trichome acylsugar production had close relatives in roots. After identifying an enzyme believed to be the first step in root acylsugar biosynthesis, the researchers began “breaking the car.” [removing one component at a time to discover how the car works].
When they knocked out the root acylsugar candidate gene, root acylsugar production vanished, leaving trichome acylsugar production untouched.
Meanwhile, when the well-studied trichome acylsugar gene was knocked out, root acylsugar production carried on as usual.
These findings offered striking proof of a suspected metabolic mirroring.
“Alongside the aboveground acylsugar pathway we’ve been studying for years, here we find this second parallel universe that exists underground,” Last said.
“This confirmed we have two pathways co-existing in the same plant,” Kerwin added.
To drive home this breakthrough, Jaynee Hart, a postdoctoral researcher and second author on the latest paper, looked closer at the functions of trichome and root enzymes.
Just as trichome enzymes and the acylsugars they produce are a well-studied chemical match, she found a promising link between root enzymes and the root acylsugars as well.
“Studying isolated enzymes is a powerful tool for ascertaining their activity and drawing conclusions about their functional role inside the plant cell,” Hart explained.
These findings were further proof of the parallel metabolic pathways that exist in a single tomato plant.
“Plants and cars are so different, yet similar in that when you open the proverbial hood you become aware of the multitude of parts and connections that make them function. This work gives us new knowledge about one of those parts in tomato plants and prompts further research into its evolution and function and whether we can make use of it in other ways,” said Pankaj Jaiswal, a program director at the U.S. National Science Foundation, which funded the work.
“The more we learn about living things — from tomatoes and other crops, to animals and microbes — the broader the opportunities to employ that learning to benefit society,” he added.
Clusters within clusters
The paper also reports a fascinating and unexpected twist concerned with biosynthetic gene clusters, or BGCs.
BGCs are collections of genes that are physically grouped on the chromosome and contribute to a particular metabolic pathway.
Previously, the Last lab identified a BGC containing genes linked to trichome acylsugars in tomato plants. Kerwin, Hart, and their collaborators have now discovered the root-expressed acylsugar enzyme resides in the same cluster.
“Usually in BGCs, the genes are co-expressed in the same tissues and under similar conditions,” said Kerwin.
“But here, we have two separate yet interlinked groups of genes. Some expressed in trichomes, and some expressed in roots.”
This revelation led Kerwin to dive into the evolutionary trajectory of Solanaceae species, with hopes to identify when and how these two unique acylsugar pathways developed.
Specifically, the researchers drew attention to a moment some 19 million years ago when the enzyme responsible for trichome acylsugars was duplicated. This enzyme would one day be responsible for the newly discovered root-expressed acylsugar pathway.
The exact mechanism that “switched on” this enzyme in roots remains unknown, paving the way for the Last lab to continue to unpack the evolutionary and metabolic secrets of the nightshade family.
“Working with Solanaceae provides so many scientific resources, as well as a strong community of researchers,” said Kerwin.
“Through their importance as crops and in horticulture, these are plants humans have cared about for thousands of years.”
For Last, these breakthroughs are also a reminder of the importance of natural pesticides, which defense metabolites such as acylsugars ultimately represent.
“If we find that these root acylsugars are effective at repelling harmful organisms, could they be bred into other nightshades, thereby helping plants grow without the need for harmful synthetic fungicides and pesticides?” Last asked.
“These are questions at the core of humanity’s pursuit of purer water, safer food and a reduced reliance on harmful synthetic chemicals.”
AbstractIf anyone is still tempted to fall for the Intelligent Design hoax, they should be asking themselves at this point, "Which is the more plausible explanation for this duplication of effort and apparent re-invention of doing something that the tomato plant could already do? Magic by an omniscient, super-intelligent supernatural designer, or an accidental gene publication followed by a mindless, unplanned natural evolutionary process in which neither intelligence nor design played a part?
Tremendous plant metabolic diversity arises from phylogenetically restricted specialized metabolic pathways. Specialized metabolites are synthesized in dedicated cells or tissues, with pathway genes sometimes colocalizing in biosynthetic gene clusters (BGCs). However, the mechanisms by which spatial expression patterns arise and the role of BGCs in pathway evolution remain underappreciated. In this study, we investigated the mechanisms driving acylsugar evolution in the Solanaceae. Previously thought to be restricted to glandular trichomes, acylsugars were recently found in cultivated tomato roots. We demonstrated that acylsugars in cultivated tomato roots and trichomes have different sugar cores, identified root-enriched paralogs of trichome acylsugar pathway genes, and characterized a key paralog required for root acylsugar biosynthesis, SlASAT1-LIKE (SlASAT1-L), which is nested within a previously reported trichome acylsugar BGC. Last, we provided evidence that ASAT1-L arose through duplication of its paralog, ASAT1, and was trichome-expressed before acquiring root-specific expression in the Solanum genus. Our results illuminate the genomic context and molecular mechanisms underpinning metabolic diversity in plants.
INTRODUCTION
Plants synthesize and store a vast array of metabolites. Essential and ubiquitous metabolites, including sugars, amino acids, and lipids, are synthesized through highly conserved general, or primary, metabolic pathways. In contrast, most of the chemical diversity observed among plants is produced through taxonomically restricted specialized metabolic pathways that use general metabolic precursors (1). Specialized metabolites are commonly synthesized and stored in dedicated cells, tissues, or organs, and serve critical roles in herbivore defense (2–5), pollinator attraction (3, 6, 7), and abiotic stress mitigation (8–10). Specialized metabolite variation influences herbivory, disease, and fitness in the natural environment (11–13), reflecting their adaptive roles.
Specialized metabolic pathways often emerge through gene duplication and divergence, co-opting enzymes and precursors from other aspects of plant metabolism, including general metabolism (14–17). Typically, enzymes involved in specialized metabolism exhibit broader substrate specificities and narrower expression patterns than those of general metabolism (15, 16, 18). However, the molecular mechanisms by which specialized metabolic pathway genes acquire their distinct expression patterns remain poorly understood, representing an important gap in our knowledge.
The genes of some specialized metabolic pathways colocalize on chromosomes into biosynthetic gene clusters (BGCs) (19, 20), which can facilitate pathway coregulation and localized metabolite production (21). Established BGCs promote coinheritance of clustered genes due to reduced recombination, thereby maintaining metabolic pathway integrity (22, 23). Within BGCs, exchange of coding or regulatory sequences, for example, through recombination, can lead to gene duplication or altered gene expression patterns (24, 25), yet the precise roles of BGCs in the evolution of specialized metabolic pathways, particularly in the context of regulatory divergence, are not fully elucidated.
Acylsugar biosynthesis is an ideal system to investigate the molecular mechanisms underlying metabolic pathway evolution. These specialized metabolites are synthesized in the tip cells of type I/type IV glandular trichomes of Solanaceae species (26–29) and protect aerial plant surfaces against herbivory, disease, and desiccation (27, 30–34). Composed of a sugar core decorated with straight or branched acyl chains, acylsugars in cultivated tomato (Solanum lycopersicum) trichomes are assembled by four clade III BAHD (BEAT AHCT HCBT1 DAT) acyltransferase enzymes, ACYLSUGAR ACYLTRANSFERASE 1 (SlASAT1; Solyc12g006330), SlASAT2 (Solyc04g012120), SlASAT3 (Solyc11g067670), and SlASAT4 (Solyc01g105580), which sequentially esterify acyl chains to a central sucrose core (35–37). Acylsugar biosynthesis also involves enzymes co-opted from general metabolism, including ISOPROPYLMALATE SYNTHASE 3 (IPMS3; Solyc08g014230) (38), ACYLSUGAR ACYL-COA SYNTHETASE 1 (AACS1; Solyc07g043630) (39), and ACYLSUGAR ENOYL-COA HYDRATASE 1 (AECH1; Solyc07g043680) (39). Notably, SlASAT1, SlAECH1, and SlAACS1 are colocalized to a trichome acylsugar BGC spanning syntenic regions of chromosomes 7 and 12 (39).
In addition to their presence in glandular trichomes, a recent study unexpectedly revealed acylsugars in the roots of cultivated tomato (40), suggesting the existence of a previously uncharacterized root-specific biosynthetic pathway. Here, we examined the structural diversity, biosynthesis, and evolutionary origin of these cultivated tomato root acylsugars.
Our results are consistent with the hypothesis that a distinct acylsugar biosynthetic pathway operates in tomato roots. Through detailed metabolite characterization, we found that cultivated tomato roots accumulate acyldissacharides that are distinct from the tri- and tetraacylsucroses synthesized in trichomes. Nuclear magnetic resonance (NMR) spectroscopic analysis demonstrated that the most abundant cultivated tomato root acylsugar has a glucosylinositol disaccharide core. Analyzing coexpression across cultivated tomato tissues, we identified a set of root-expressed paralogs of characterized trichome acylsugar pathway genes. We functionally characterized SlASAT1-LIKE (SlASAT1-L; Solyc07g043670), the root-expressed paralog of SlASAT1, the first core trichome acylsugar biosynthesis pathway gene, yielding results consistent with a role early in root acylsugar biosynthesis. First, genetic ablation of SlASAT1-L led to loss of detectable root acylglycosylinositols, with no impact on trichome acylsucroses, providing strong evidence for separate biosynthetic pathways. Second, consistent with the hypothesis that SlASAT1-L catalyzes the first step of acylglycosylinositol biosynthesis, the enzyme acylated myo-inositol, but not sucrose, in vitro.
Notably, root-expressed SlASAT1-L and paralogs of two other trichome acylsucrose biosynthetic genes are nested within the previously identified trichome acylsugar BGC (39). We analyzed synteny and coexpression within the BGC, revealing that ASAT1-L arose via ASAT1 duplication and was originally trichome-expressed before evolving root-specific expression in a subset of Solanum species. Further, we found a correlation between the spatial expression pattern of ASAT1-L and the site of inositol-based acylsugar accumulation among extant Solanum species. Our findings demonstrate that gene duplication, regulatory divergence, and enzyme evolution within a BGC can modify the cell- or tissue-specific localization of a biosynthetic pathway, shedding light on the molecular mechanisms contributing to metabolic diversity in plants.
The Unintelligent Designer: Refuting The Intelligent Design Hoax
ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.
Available in Hardcover, Paperback or ebook for Kindle
The Malevolent Designer: Why Nature's God is Not Good
This book presents the reader with multiple examples of why, even if we accept Creationism's putative intelligent designer, any such entity can only be regarded as malevolent, designing ever-more ingenious ways to make life difficult for living things, including humans, for no other reason than the sheer pleasure of doing so. This putative creator has also given other creatures much better things like immune systems, eyesight and ability to regenerate limbs that it could have given to all its creation, including humans, but chose not to. This book will leave creationists with the dilemma of explaining why evolution by natural selection is the only plausible explanation for so many nasty little parasites that doesn't leave their creator looking like an ingenious, sadistic, misanthropic, malevolence finding ever more ways to increase pain and suffering in the world, and not the omnibenevolent, maximally good god that Creationists of all Abrahamic religions believe created everything. As with a previous book by this author, "The Unintelligent Designer: Refuting the Intelligent Design Hoax", this book comprehensively refutes any notion of intelligent design by anything resembling a loving, intelligent and maximally good god. Such evil could not exist in a universe created by such a god. Evil exists, therefore a maximally good, all-knowing, all-loving god does not.
Illustrated by Catherine Webber-Hounslow.
Available in Hardcover, Paperback or ebook for Kindle
Illustrated by Catherine Webber-Hounslow.
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