New sugar transport gene evolved in yeast?

Mixing genes does not equal evolution!

by ,

Published: 23 July 2019 (GMT+10)

Introduction

sugar-transport-gene
A. Different regions of the genes SeMALT1, 3, and 4 which were fused to form the SeMALT413 gene. B. The three- dimensional protein structure of the SeMALT413 protein. Green gene/protein segments denote parts coming from the SeMALT1 gene, blue segments denote parts coming from the SeMALT3 gene, and orange segments denote parts coming from the SeMALT4 gene.
Credit: Ref. 3

A research team at the department of Biotechnology at Delft University of Technology in the Netherlands claims to have ‘evolved’ a species of yeast (Saccharomyces eubayanus)1 to digest a complex sugar called maltotriose. After exposing the yeast to high levels of ultraviolet light, they discovered a hybrid gene that gave it this new ability. The hybrid gene codes for a transporter protein which allows maltotriose into the cell. The yeast strain with the newly engineered gene was capable of increased maltose and maltotriose fermentation, which can be used in the brewing industry.

All living things, from single-celled bacteria to multi-trillion-celled-humans, have a cellular membrane that prevents things from leaking out of or from entering the cell. In order to live, food has to be brought into the cell through that membrane. Thus, all species have transport proteins that help to bring things into the cell. The genes responsible for transporting sugars into the yeast cell are called SeMALT genes. There is a diversity of such genes found among the many yeast species. The new gene, SeMALT413, is a hybrid of three already existing genes in S. eubayanus. It supposedly arose via non-reciprocal translocations (i.e. specific parts of these other genes were copied and moved to a new location where they were combined).

This new gene is the product of laboratory manipulation but is being used as ‘proof of evolution’. Evolutionists claim that a gene with a new structure has evolved in the lab, giving the yeast the ability to metabolize a new food source. This is an example of neofunctionalization, whereby a new function arises in a pre-existing gene family. It is also an example of something we heralded several years ago in the article Can Mutations Create New Information? Yes, new functions can arise in living things, but no, this is not evidence of evolution. Christians can often get caught flat-footed when they see claims like this. But by carefully analyzing what words are being used, we can learn to see through the deception.

To create this new ability, yeast cells were first grown in the presence of the sugar glucose. They were then transferred to a medium containing maltotriose as the sole carbon source. Mild UV-mutagenesis was applied to induce mutations, after which maltotriose depletion was observed in some media samples. Two strains that could digest maltotriose were isolated.2,3

What kind of mutations really happened?

Despite the sensationalist claims, upon closer examination we must conclude there is no decisive evidence to support evolution here. After all, the yeast remained yeast, and the only thing that happened was that a hybrid gene came about through recombination.

During the UV-mutagenesis experiment, they discovered five single nucleotide polymorphisms (SNPs) and four copy number variations (CNVs). The SNPs had never been linked to maltotriose utilization previously, and the authors did not describe how these SNPs function, so we are left a bit in the dark about the significance of these changes. The copy number variations affected several regions in the genome of S. eubayanus containing SeMALT genes. Specifically, the new SeMALT413 gene is made up of duplicated segments of three existing SeMALT genes, numbers 1, 3, and 4. These came from chromosomes 2 (part of SeMALT1), 8 (part of SeMALT3), and 16 (two different parts of SeMALT4). The structure of the SeMALT413 protein is a composite of alpha-helixes from the three original SeMALT genes. Interestingly, it is highly similar to that of the major facilitator superfamily, which is a large family of membrane transporter proteins.4,5

Implications

For large-scale macroevolution to happen, great quantities of new genetic information, contained within many new gene families, must be built up over billions of years. A mechanism for this was not demonstrated in this study. While it is true that a ‘new gene’ was stitched together from parts of other genes, it did not create entirely new genetic information, such as new exons, which could possibly code for a new protein domain.6 As the authors of the study themselves say, what happened was merely parts of existing genes were shuffled around to form a new gene.

The genetics of sugar transport in the various yeast species are complex. Closely related species can carry a diversity of transporters, enabling some to import some sugars but not others. To make things even more complicated, Saccharomyces pastorianus is a hybrid of two other yeast species, Saccharomyces cerevisiae and S. eubayanus (the subject of this article). Entire chromosomes, including the genes for the transporter proteins, are identical between the parental species and the hybrid. In the same way that scientists no longer talk about the E. coli “genome”, because different strains of this bacterium carry different genes, we should consider these yeast species as part of a ‘holobaramin’7 that share a ‘pan-genome’. In other words, they all belong to the same ‘created kind’.

We know that Se MALT413 can transport maltotriose across the cell membrane in S. eubayanus. Where did this ability come from? S. cerevisiae has a protein called Sc Agt1, which is also capable of maltotriose transport.8 The amino acids in the active center of this protein, which are critical for maltotriose transport, are also present in Se MALT3 in S. eubayanus. But Se MALT3 itself alone is incapable of transporting maltotriose. Interactions between different amino acid residues from Se MALT1 and 4 are necessary for it to do so. It was the combination of these features which allowed Se MALT413 to do what it does.

Is the SeMALT413 gene really a new gene? Does it really represent new genetic information in S. eubayanus? A variant of the previously mentioned Sc AGT1 gene happens to be present also in S. pastorianus, albeit in a truncated, non-functional form.9 This implies that a gene, which is capable of transporting maltotriose was passed on from S. eubayanus to S. pastorianus, which underwent subsequent partial deletion.

However, despite the presence of this truncated and seemingly useless gene, S. pastorianus is still capable of transporting maltotriose into the cell, using two other genes, namely LgAGT1 and SpMTY1. LgAGT1 shows an 85% sequence similarity to the S. cerevisiae Sc AGT1 gene10, indicating that they are functional homologs of one another. Furthermore, LgAGT1 itself is a maltotriose transporter, and is also present on the S. eubayanus chromosome 15 of S. pastorianus. This gene is also present in the industrial S. eubayanus isolate yHRVM108, which is capable of maltotriose transport.11 This means that at one point in its history, S. eubayanus contained a gene which was capable of fulfilling the role of maltotriose transport, but was either truncated or lost.

Besides this, the gene SpMTY1 is located on the S. eubayanus chromosome 7 of S. pastorianus and displays segmental sequence identity with SeMALT genes, demonstrating their homology (and thus similar functionality) with one another.12 The fact that LgAGT1 is located specifically on the S. eubayanus chromosome of S. pastorianus indicates that they were once present in S. eubayanus but were subsequently lost.

In several species of Saccharomyces, the MALT transporter genes are located in the gene-poor and repeat-rich subtelomeric regions of chromosomes. The repeat regions increase the probability of genetic recombination, thereby increasing the diversity of gene families in this region. Recombination in this area is actually quite common in yeast.13 This could well be a designed feature intended to facilitate adaptation to different food sources.

In an unrelated study, mutations in E. coli allowed it to metabolize citrate under aerobic conditions. Normally, citrate metabolism is turned off when oxygen is present. The researchers found that the citrate transporter protein gene had been duplicated and had come under the control of a promoter which was active in the presence of oxygen. This gene was also duplicated several times, thereby allowing increased citrate uptake. A third mutation in the regulatory gene arcB up-regulated the TCA cycle, thereby making more efficient use of citrate when taken up into the cell.14 Yet, as in the other examples, complex rearrangements of biological information, even ones that confer a new ‘function’ on the cell, are not evidence for long-term directional evolutionary changes that would create a brand new organism. The changes we see fit neatly into the idea that God created life to dynamically respond to various environments.

Conclusion

This is yet again a false alarm. While the study was a fine piece of work, with useful industrial application in the brewing industry, it only demonstrated that existing genetic information can be reshuffled. Yes, this brought about a new function, in a recombined gene, but this is well within the design parameters of life. In fact, being that this gene family is located in a region of the genome with an exceptionally high recombination rate, it appears that God engineered yeast with the ability to adapt to new food sources as the need arises. A new member of an existing gene family was created, but not a new gene family, and similar versions of this gene have already been found in closely related yeast species. It does not explain the origin of any kind of entirely novel genetic information, and the information changes appear to be controlled, not random. The creation of genetic information across the spectrum of life can be ascribed to God alone, who has wonderfully created and designed everything. In this case, the information He created has been rearranged to help this yeast eat something new. Instead of evidence of evolution, this is a testimony to the brilliant foresight of the God of creation.

References and notes

  1. More specifically, Saccharomyces eubayanus strain CBS 12357T. Return to text.
  2. Delft University of Technology, Researchers witness the emergence of a new gene in the lab (2019, April 9). Retrieved from https://www.tudelft.nl/en/2019/tu-delft/researchers-witness-the-emergence-of-a-new-gene-in-the-lab/ Return to text.
  3. Brouwers, N. et al. In vivo recombination of Saccharomyces eubayanus maltose-transporter genes yields a chimeric transporter that enables maltotriose fermentation. PLoS Genet 15(4):e1007853, 2019. Return to text.
  4. Yan, N. Structural biology of the major facilitator superfamily transporters. Annu Rev Biophys 44:257–283, 2015. Return to text.
  5. Pao, S.S., Paulsen, I.T., and Saier, M.H. Jr. Major facilitator superfamily. Microbiol Mol Biol Rev 62(1):1–34, 1998. Return to text.
  6. See the discussion on protein domains in Carter, R.W., Can biologically active sequences come from random DNA? J Creation 31(3):82–89, 2017. Return to text.
  7. A baramin refers to a created kind, as described in Genesis 1. A baramin contains species which are all related to each other and have a common ancestor. A holobaramin refers to the complete set of known organisms which belong to a given baramin. Return to text.
  8. Alves, S.L. et al. Molecular analysis of maltotriose active transport and fermentation by Saccharomyces cerevisiae reveals a determinant role for the AGT1 permease. Appl Environ Microbiol. 74:1494–1501, 2008. Return to text.
  9. Vidgren, V., Huuskonen, A., Virtanen, H., Ruohonen, L., Londesborough, J. Improved fermentation performance of a lager yeast after repair of its AGT1 maltose and maltotriose transporter genes. Appl Environ Microbiol 75:2333–2345, 2009. Return to text.
  10. Vidgren, V. and Londesborough, J. Characterization of the Saccharomyces bayanus-type AGT1 transporter of lager yeast. J Inst Brew 118:148–151, 2012. Return to text.
  11. Baker, E.P. and Hittinger, C.T. Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function. bioRxiv: 431171, 2018. Return to text.
  12. Cousseau, F., Alves, S Jr., Trichez, D., Stambuk, B. (2013) Characterization of maltotriose transporters from the Saccharomyces eubayanus subgenome of the hybrid Saccharomyces pastorianus lager brewing yeast strain Weihenstephan 34/70. Lett Appl Microbiol 56:21–29, 2013. Return to text.
  13. Brown, C.A., Murray, A.W., and Verstrepen, K.J. Rapid expansion and functional divergence of subtelomeric gene families in yeasts. Curr Biol 20(10):895–903, 2010. Return to text.
  14. Blount, Z.D., Barrick, J.E., Davidson, C.J., Lenski, R.E. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489(7417):513–8, 2012. Return to text.

Helpful Resources

Readers’ comments

Joshua W.
I’m a little confused after reading this article. So this should not be considered “new” information because other similar strains of yeast also have a similar function? Also, as many articles from CMI have argued before, and I would agree with this, mutations often, if not always, end up in a loss of information. The yeast may now be adapted to intake the different sugar, but did it lose anything in the process?
Matthew Cserhati
Hello Joshua,
Thanks for your question.
The way I would describe this is that already existing genetic information was shuffled around between different strains (sub-species) of yeast. In this case, the genetic units being shuffled around are not whole genes. Rather they are smaller segments of genes, which may code for functional sub-units of proteins (i.e. an enzyme) called domains. So, the gene itself may be new, but the regions coding for protein domains are not new. Imagine a deck of cards with 13 figures, ace to king and the four suits. We can combine the suits and the figures, but we will never produce an "earl of stars". Lastly, you are correct, that since already existing genetic information was merely being shuffled around, this way no genetic information was actually lost.
The Bible doesn't say that God created static genomes or fixed species. God could have designed certain genetic elements for directed adaptation. An example is the hypervariable regions which form the antigen-binding site on the immunoglobin molecule. This is how new antibodies can be formed to fight antigens invading the body. Similarly, the SeMALT genes in the subtelomeric regions of the chromosomes they are located at can give rise to new variants to be able to use new types of sugar molecules, in this case, maltotriose.
The following article describes in detail the relationship between mutations and genetic information.
Mike D.
Ironically when you break all this & other stuff evolutionist do to present claims like this. It just proves Intelligent Design. Intelligent humans were involved in this process all along the way. It was not Random trial & error. None of their stuff ever it. It's always done by Intelligent Designer scientist. Plus it never became non yeast. Same when working with corn, wheat, roses etc. It always proves ID not Random trial & error. Then we just search for who is the real ID. Sure can't be an idol made by man's own hands. Bible even describes that. So you search for the true & real ID. Biblical apologetics & it's inerrancy will lead One to Triune Godhead with Jesus as CREATOR per John 1:1-5 & Col chapter 1.

I find it ironic & sad they don't catch the irony of what it really proves so easily bottom line.

Wake up evolutionist! It's true for all your experiments & claims like this. You as Intelligent Humans guided the whole thing thus proving ID & not Random trial & error!

It's really that Simple!

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