Sunday, 28 August 2022

Creationism In Crisis - More Bad News for Creationists as Scientists Use the TOE to Work Out How Mucus Evolved

The evolution of mucus: How did we get all this slime? - University at Buffalo

Fig. 1. Novel and previously known mucin genes in select mammalian species.
Phylogeny on the left represents the relationship between the species analyzed here [human (hg38), mouse (mm10), cow (bosTau9), and ferret (musFur1)]. Schematic karyotypes show the chromosomes in each species that harbor mucin genes. Mucin gene locations are indicated on each chromosome. Ancestral mucin genes that are orthologous in the four genomes are indicated in blue fonts. Lineage-specific mucins are indicated in green fonts. Mucin genes found within the SCPP gene family, all of which, except for MUC7, are lineage-specific are indicated in pink fonts. Note: Some of the orthologous genes carry different names in different species. For example, rodent Muc3 is orthologous to human MUC17. For those genes, we indicated in parentheses following the official gene annotation the name of the likely human ortholog based on sequence similarity and synteny. In ferrets, the “S” proceeding the putative chromosome number indicates on which Hi-C scaffold the mucin genes were found.

Possibly not the most fascinating of subjects, especially if you're a Creationist fraud trying to convince your dupes that the theory of evolution is a theory in crisis due to not being able to explain stuff like the evolution of proteins, but scientists at the University of Buffalo, New York, USA, have worked out how the various forms of mucus, or slime, evolved.

And guess what! The Theory of Evolution was absolutely essential to understanding the process!

And even worse for creationist frauds who are trying to convince their dupes that the second law of thermodynamics somehow means that no new information can arise without the assistance of a magic creator, is the news that this evolution involved examples of gene doubling where a mistake in replication - a mutation - has provided the process of evolution with genetic 'information' that can be changed without harming the carrier of that mutation. In other words, mutation followed by natural selection has increased the amount of information in the genome by perfectly natural processes, with no need to include magic or a magic creator in the explanation.

The News release by Charlotte Hsu, from the University of Buffalo explains how the scientists made this discovery:
From the slime coating slugs to the saliva in our mouths, many slippery bodily fluids contain mucus. So how did this marvel of biology evolve?

In mammals, the answer is many times, and often in a surprising way, according to a new study on proteins called mucins. These molecules have a variety of functions, but as a family, they are known as components of mucus, where they contribute to the substance's gooey consistency.

Through a comparison of mucin genes in 49 mammal species, scientists identified 15 instances in which new mucins appear to have evolved through an additive process that transformed a non-mucin protein into a mucin.

The scientists propose that each of these “mucinization” events began with a protein that wasn’t a mucin. At some point, evolution tacked a new section onto this non-mucin base: one consisting of a short chain of building blocks called amino acids that are decorated with sugar molecules. Over time, this new region got duplicated, with multiple copies added on to elongate the protein even further, making it a mucin.

The doubled regions, called “repeats,” are key to a mucin’s function, say University at Buffalo researchers Omer Gokcumen and Stefan Ruhl, the senior authors of the study, and Petar Pajic, the first author.

The sugars coating these sections protrude outward like the bristles of a bottle brush, and they bestow mucins with the slimy property that’s vital to many important tasks that these proteins carry out.

The research was published on Aug. 26 in Science Advances.

I don’t think it was previously known that protein function can evolve this way, from a protein gaining repeated sequences. A protein that isn’t a mucin becomes a mucin just by gaining repeats. This is an important way that evolution makes slime. It’s an evolutionary trick, and we now document this happening over and over again.

I think this paper is really interesting. It’s one of those times where we got lucky. We were studying saliva, and then we found something that’s interesting and cool and decided to look into it.

Professor Omar Gokcumen, PhD, senior author
Department of Biological Sciences
University at Buffalo,
The State University of New York, Buffalo, NY, USA.

The repeats we see in mucins are called ‘PTS repeats’ for their high content of the amino acids proline, threonine and serine, and they aid mucins in their important biological functions that range from lubricating and protecting tissue surfaces to helping make our food slippery so that we can swallow it. Beneficial microbes have evolved to live on mucus-coated surfaces, while mucus can at the same time also act as a protective barrier and defend against disease by shielding us from unwanted pathogenic intruders.

Not many people know that the first mucin which had been purified and biochemically characterized came from a salivary gland. My lab has been studying mucins in saliva for the last 30 years, mostly because they protect teeth from decay and because they help balance the microbiota in the oral cavity.

Stefan Ruhl, PhD, co-senior author
Interim dean of the University of Buffalo School of Dental Medicine and professor of oral biology
Department of Oral Biology, School of Dental Medicine
University at Buffalo, The State University of New York, Buffalo, NY , USA.
While studying saliva, the team noticed that a small salivary mucin in humans called MUC7 was not present in mice. The rodents did, however, have a similarly sized salivary mucin called MUC10. The scientists wanted to know: Were these two proteins related from an evolutionary perspective?

We think that somehow that tear gene ends up repurposed. It gains the repeats that give it the mucin function, and it’s now abundantly expressed in mouse and rat saliva.

Professor Omar Gokcuman
The answer was no. But what the research uncovered next was a surprise. While MUC10 did not appear to be related to MUC7, a protein found in human tears called PROL1 did share a portion of MUC10’s structure. PROL1 looked a lot like MUC10, minus the sugar-coated bottlebrush repeats that make MUC10 a mucin.

How new gene functions evolve is still a question we are asking today. Thus, we are adding to this discourse by providing evidence of a new mechanism, where gaining repeated sequences within a gene births a novel function.

I think this could have even broader implications, both in understanding adaptive evolution and in possibly explaining certain disease-causing variants. If these mucins keep evolving from non-mucins over and over again in different species at different times, it suggests that there is some sort of adaptive pressure that makes it beneficial. And then, at the other end of the spectrum, maybe if this mechanism goes ‘off the rails’ — happening too much, or in the wrong tissue — then maybe it can lead to disease like certain cancers or mucosal illnesses.

Petar Pajic, first author
Department of Biological Sciences and Department of Oral Biology, School of Dental Medicine
University at Buffalo, The State University of New York, Buffalo, NY, USA.
The scientists wondered whether other mucins might have formed the same way. They began to investigate and discovered multiple examples of the same phenomena. Though many mucins share common ancestry among various groups of mammals, the team documented 15 instances in which evolution appeared to have converted non-mucin proteins into mucins via the addition of PTS repeats.

My team has been studying mucins for many decades, and my collaboration with Dr. Gokcumen has brought this research to a new level by revealing all these exciting novel insights into their evolutionary genetics. At this advanced stage of my career, it is also immensely gratifying to see that the flame of scientific curiosity is being carried on by a new generation of young investigators like Petar Pajic.

Stefan Ruhl, PhD.
And this was “with a pretty conservative look,” Gokcumen says, noting that the study focused on one region of the genome in a few dozen mammal species. He calls slime an “amazing life trait,” and he’s curious whether the same evolutionary mechanism might have driven the formation of some mucins in slugs, slime eels and other critters. More research is needed to find an answer.

The study on mucins demonstrates how a long-time partnership between evolutionary biologists and dental researchers at UB is yielding new insights into genes and proteins that are also important to human health.
The study also shows how essential is an understanding of the Theory of Evolution to making sense of biology. To a biologist, it makes no difference whether we are looking at the evolution of genes that give rise to new species or subspecies or the evolution of genes that give rise to new proteins, the process is essentially the same.

Copyright: © 2022 The authors.
Published by American Association for the Advancement of Science.
Open access. (CC BY-NC 4.0)
In the abstract to their open access paper published in Science Advances, the team again emphasise the importance of the TOE to understanding how proteins, not just species, evolved:
Abstract

How novel gene functions evolve is a fundamental question in biology. Mucin proteins, a functionally but not evolutionarily defined group of proteins, allow the study of convergent evolution of gene function. By analyzing the genomic variation of mucins across a wide range of mammalian genomes, we propose that exonic repeats and their copy number variation contribute substantially to the de novo evolution of new gene functions. By integrating bioinformatic, phylogenetic, proteomic, and immunohistochemical approaches, we identified 15 undescribed instances of evolutionary convergence, where novel mucins originated by gaining densely O-glycosylated exonic repeat domains. Our results suggest that secreted proteins rich in proline are natural precursors for acquiring mucin function. Our findings have broad implications for understanding the role of exonic repeats in the parallel evolution of new gene functions, especially those involving protein glycosylation.

One can almost feel sorry for Creationists the way science keeps on refuting their core beliefs. But then they should be so well versed in coping with a reality which differs markedly from what their cult leaders tell them, that they should have little difficulty coping with yet another casual refutation of their superstition by a team of scientists who had no intention of doing so, but were merely discovering the biological truth and using a well-established principle of biology to interpret the facts they discovered.

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