Today’s New Reason To Believe

Posted by Fazale ‘Fuz’ Rana, Ph.D.

New Insight into the Cell’s Quality-Control Systems Provided Added Evidence for Design

It’s easy to take garbage men for granted—until they go on strike or can’t do their job properly, which is the case in Naples, Italy.

Getting rid of trash is essential for well-run households, businesses, and communities. Piles of waste are an unpleasant health hazard.

Disposing of garbage is just as necessary for cells as it is for municipalities. Cells have to get rid of their molecular debris and waste to function properly. In most cases, the cell is able to remove its biomolecular rubbish. But in some cases, it can’t. The consequences can be devastating. Accumulating piles of biochemical waste are a health hazard for cells too. As a case in point, some neurodegenerative diseases, like Huntington’s, involve the build-up of biochemical waste in the form of protein aggregates.

Understandably, biologists are interested in trying to learn how and why protein waste accumulates in cells and what can be done to eliminate it. New work by Stanford University scientists published in Nature provides important insight into how protein waste is processed by the cell. This new knowledge suggests a possible strategy to help cells clear out intractable biomolecular garbage. This new understanding also adds to the evidence that life stems from a Creator’s hand.

Last week I described the make-up of the cell’s garbage and the central cogs in the cell’s waste-disposal machinery. This week I’ll describe the new research by the team of cell biologists from Stanford University and discuss its implications.

Protein Waste Disposal

Much of the cellular rubbish consists of protein aggregates. Proteins are chain-like molecules that fold into precise three-dimensional structures. A protein’s three-dimensional architecture determines its function. Proteins play a key role in virtually every cellular function and help form nearly every cellular structure.

Cells constantly make and destroy proteins. Specialized proteins used in particular activities are manufactured only when needed. Once these proteins have outlived their usefulness, the cell breaks them down into their constitutive amino acids. However, proteins that play a central role in the cell’s operation are produced on a continual basis. These proteins inevitably suffer damage from use and must be destroyed and replaced with newly made proteins. Faulty manufacturing also produces protein waste. The folding of newly made protein chains into their native three-dimensional architecture is error-prone. Misfolded proteins must be removed because they tend to form aggregates inside the cell.

Damaged or misfolded proteins are tagged with a small protein molecule called ubiquitin. These molecular tags inform the cell’s machinery that the damaged protein needs to be destroyed. A massive protein complex called a proteasome demolishes damaged, ubiquitinated proteins.

Accumulation of Protein Waste and Quality Control

Most unneeded, damaged, and misfolded proteins are readily cleared by the cell’s protein degradation system. However, some are not. These problematic proteins interact with each other to form large insoluble aggregates inside the cell. Most biologists think the failure of the cell’s machinery to eliminate these aggregated proteins stems from faulty quality-control operations in the cell.

As I describe in The Cell’s Design, every key stage, including the final step, of protein production is accompanied by quality-control checkpoints. These include the final step in the process. The proteasome eliminates any faulty proteins. The placement of these quality-assurance checkpoints occurs at strategic stages in the production process in a way that ensures reliable protein production while generating manufacturing efficiency.

In The Cell’s Design, I assert that biochemical quality assurance exemplifies the remarkable ingenuity that defines the cell’s chemistry and reinforces the conclusion that life has a supernatural basis. Effective and efficient quality-control procedures don’t just happen. Rather, they are characterized by intentional foresight. Sound quality-control systems require careful planning, a detailed understanding of the manufacturing process, the product, and the way that the product will be used. All of these features are evident in the quality-control activities in the cell.

Still, the inability to effectively eliminate aggregated proteins undermines the case for biochemical intelligent design if it is due to ineffective quality-control systems. But as new work reveals, the protein degradation process is much more complicated than previously thought.

Two Cellular Locales for Protein Waste Management

Stanford cell biologists performed a series of elegant experiments that revealed two cellular locales for protein waste disposal. The first region is situated near the juncture of the nucleus and the endoplasmic reticulum. This site is rich in proteasomes. Proteins sent to this location are highly ubiquinated and soluble. The proteasomes readily degrade or refold these proteins. (See my article from last week.)

The other site, which is located near the exterior of the cell, consists of insoluble protein deposits. Proteins sent to this location are lightly ubiquinated and insoluble. These proteins form insoluble aggregates that can’t be eliminated by the cell. Over time these deposits accumulate in the cell.

Proteins found in the second site include those associated with the onset of Huntington’s disease. They also includes proteins that would normally be cleared from the cell, but fail to be adequately ubiquinated because of stress. Under stressful conditions, a large number of proteins unfold, overwhelming the protein degradation system. The ageing process also contributes to proteins found in this site.

Production of insoluble protein deposits does not appear to be a malfunction of the cell’s quality-control systems. Instead it represents an elegant strategy for managing cellular waste. By piling insoluble protein aggregates into these deposits, the cell’s quality-control operations have effectively sequestered these harmful aggregates from the cell’s machinery, minimizing their harmful effects.

The authors of this study also note that the formation of these deposits provides a means to limit the transmission of insoluble protein aggregates to daughter cells generated from cell division. If distributed throughout the cell, a significant portion of the insoluble protein aggregates would be transferred to both daughter cells every time cell division took place. By incorporating all of the insoluble proteins into a single deposit, only one daughter cell is saddled with these potentially harmful materials. The other daughter cell winds up with a pristine cytoplasm.

Additionally, the Stanford researchers detected markers that flag the insoluble protein aggregates for autophagy). This process involves the breakdown of the cell’s own components by its digestive machinery. Autophagy provides a separate means to clear misfolded proteins from the cell independent from proteasomes.

Based on this new research, the formation of insoluble protein deposits no longer appears to be due to the failure of the cell’s quality-control systems. Instead it reveals that the quality assurance operations in the cell are far more complex and sophisticated than originally thought. The generation of insoluble protein aggregates serves a protective function for the cell and also provides a pathway to eliminate intractable protein conglomerations from inside the cell.

Like garbage in the streets of Naples, the biochemical evidence for intelligent design keeps piling up.

Fazale ‘Fuz’ Rana, Ph.D.

Rational Design of Novel Enzyme Highlights Biochemical Design

In 1978, three scientists (Hamilton Smith, Werner Arber, and Daniel Nathans) were awarded the Nobel Prize in Physiology or Medicine for the discovery of restriction enzymes and their applications. These proteins make genetic engineering possible. They have also contributed to the wave of advances that led to the sequencing of the human genome and to the emergence of other biotechnologies.

Restriction enzymes (or endonucleases) are important for another reason. They represent an interesting example of a chicken-and-egg biochemical system and comprise part of the collection of evidence that indicates life must stem from a Creator. Recent work on these proteins highlights this point.

Endonucleases are a family of proteins. This class of biomolecules cleaves DNA. Restriction endonucleases cut both strands of DNA at specific nucleotide sequences, called restriction sites. Specifically, restriction endonucleases protect the cell from foreign DNA, like viruses, by cutting the invading DNA into fragments.

These vital biomolecules occur in conjunction with proteins (called DNA methylases) that attach methyl groups to the same DNA sequences that would normally be cleaved by restriction endonucleases. When these sequences are methylated, restriction endonucleases cannot cut them. Restriction sites of the bacterial DNA are methylated to completely protect the bacterial DNA from being chopped up by its own restriction endonulceases. Foreign DNA, however, is not afforded this same protection.

DNA methylases and restriction endonucleases form a chicken-and-egg pair. Restriction endonucleases would destroy bacterial DNA without DNA methylases. On the other hand, if bacteria did not utilize restriction endonucleases there would be no need for DNA methylases. These two proteins are interdependent and must come into existence simultaneously.

New research by scientists from the Indian Institute of Science (Bangalore, India) helps demonstrate why biochemical systems like restriction endonucleases require the work of an intelligent Agent. These researchers performed experiments to understand the origin of restriction endonucleases from an evolutionary perspective. They also wanted to develop a strategy for engineering novel, nonnatural restriction endonucleases.

Evolutionary biologists think restriction endonucleases evolved from non-specific endonucleases through point mutations in the gene region that codes the DNA binding site on the protein surface. According to this model, once specificity was established recombination and genetic shuffling of the DNA sequences that encode the DNA recognition sites would have generated new restriction endonucleases with different specificities.

To explore this possibility the research team attempted to engineer a highly specific restriction endonuclease from one (R. KpnI) that promiscuously binds to DNA. To accomplish this goal, the scientists employed a rational design strategy to determine which amino acids in the R. KpnI structure to change. These workers had to make use of the detailed understanding of this protein’s structure and functional properties in order to develop the redesign strategy.

They successfully achieved their intended goal by replacing an aspartic acid residue with an isoleucine moiety at amino acid position 163 in the R. KpnI protein chain.

This research illustrates how carefully-thought-through single amino acid substitutions can alter the specificity of restriction endonucleases. This is important work that paves the way to engineer novel, nonnatural restriction enzymes that can expand the arsenal of tools available to molecular biologists and biochemists.

The researchers involved in this study also interpreted their success as support for the evolutionary origin of restriction enzymes with point mutations ushering in the first stage in the molecular evolution of these proteins. At first glance, this interpretation seems warranted.

Still, it’s important to keep in mind that the production of the highly specific restriction endonuclease from the original promiscuous protein required intelligent input from a team of highly trained biochemists who relied on the past work of other highly accomplished scientists. In a sense, this study empirically demonstrates that protein “evolution” requires the work of an intelligent Agent.

It’s also important to note that the researchers didn’t design the companion methylase protein. This protein isn’t necessary for most biotechnology applications. But without the methylase cohort, the reengineered restriction endonuclease would wreck havoc in vivo, destroying DNA that comprises the bacterial genome.

It’s very unlikely that a restriction endonulcease and its partner methylase would simultaneously appear in an evolutionary scenario. These coordinated events would require that changes in the restriction endonuclease would take place at exactly the same time as corresponding changes in the methylase. The only way for coordinated changes like this to happen is under the auspices of an intelligent Agent.

As I point out in my new book The Cell’s Design, human engineers frequently encounter chicken-and-egg problems when designing systems and processes. Everyday experience teaches that chicken-and-egg systems can come to fruition only through intentional planning and implementation. Chicken-and-egg systems, therefore, serve as a potent indicator of intelligent design.

I describe several other examples of chicken-and-egg systems in The Cell’s Design.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

New Study Uncovers More Evidence for Biochemical Optimization and Intelligent Design

My new favorite drink is Coke Zero. I love how this zero-calorie soda tastes like the real thing, without any of the calories.

The close similarity between these two colas has spawned one of the more inventive advertising campaigns with the Coke big-wigs looking for a lawyer to sue themselves for taste infringement, since Coke Zero tastes so much like Coca Cola.

Sometimes two things seem to be indistinguishable, even though they really are quite different.

As I discussed last week, biochemists have recently come to recognize that biochemical synonyms—synonymous codons that specify the same amino acid in the genetic code—are actually distinct even though they have long been regarded as indistinguishable. It turns out that some codons are better suited than others for producing functional proteins. Biochemists refer to these preferred biochemical synonyms as optimal codons.

A new study demonstrates that the usage of optimal codons appears to be optimized as well, providing added evidence that life stems from the work of a Creator. Last week I presented the background information necessary to appreciate this new insight. This week I describe the research and discuss its implications.

Genetic Code

As I discussed last week, the genetic code constitutes a set of rules that translate the information stored in the nucleotide sequences of DNA into the amino acid sequences of proteins. Nucleotide triplets called codons represent the fundamental units of the genetic code.

Sixty-four codons make up the genetic code. Because the genetic code only needs to encode twenty amino acids, some of the codons are redundant. That is, different codons signify the same amino acid. In fact, up to six different codons specify some amino acids. Other amino acids are represented by only one codon.

Synonymous and Nonsynonymous Mutations

A mutation refers to any change that takes place in the DNA nucleotide sequence. Substitution mutations are one common type. When a substitution mutation occurs, one (or more) of the nucleotides in the DNA strand is replaced by another nucleotide. Sometimes substitution mutations generate a new codon that specifies the same amino acid as initially encoded. Biochemists refer to this type of change as a synonymous mutation. When a mutation produces a codon that specifies a different amino acid, it’s called a nonsynonymous mutation.

Nonsynonymous mutations can be deleterious if they affect a critical amino acid or if they significantly alter the chemical and physical profile along the protein chain. If the substituted amino acid possesses dramatically different physicochemical properties from the native amino acid, the protein folds improperly. This improper folding impacts the protein, yielding a biomolecule with reduced or even lost function.

Biochemists used to think that synonymous mutations had no impact whatsoever on protein structure, and hence function, since the amino acid sequence specified by the synonymous change would be identical.

Recently, biochemists have recognized that their views about synonymous changes were wrong. Even though the amino acid sequence doesn’t change, the protein structure can be altered. This altered structure stems from differences in the folding of the protein chain due to differences in the rate of protein production. Synonymous codons are read at differing rates. And the folding pattern will change depending upon the speed of protein construction.

Additionally, some synonymous codons are more likely to be misread by the cell’s machinery than others. So even though the information needed to make a particular protein isn’t changed, the wrong amino acid still may be introduced into the protein chain because of the codon used. This error, of course, can lead to structural and functional abnormalities in that protein, just as if a nonsynonymous change had occurred.

In either case, misfolded proteins can result. And this misfolding has disastrous consequences for the cell.

Misfolded Proteins

Misfolded proteins can cause profound problems for the cell. Their negative consequences extend beyond loss of function for the misfolded protein. Improperly folded proteins have a global impact on cellular health. These deformed proteins tend to form aggregates inside the cell, fouling up its inner workings. Biochemists think that many neurodegenerative diseases may have an etiology that involves aggregates formed from misfolded proteins. Misfolded proteins can also spread the misery to properly folded proteins. Once a protein has adopted a nonnative structure it can induce structurally-intact proteins to become improperly folded, enticing them to join the aggregated mess inside the cell. (As the biblical saying goes, “A little leaven, leavens the whole lump of dough.”)

In fact, even one improperly folded protein is enough to destabilize the ensemble of proteins inside a cell. (Go here for a technical article about the effect of misfolded proteins on global protein stability.) If all these problems weren’t enough, misfolded proteins can even disrupt cell membranes.

Optimal Codons are Optimally Distributed in Gene Sequences

Motivated by the impact of synonymous codons on protein folding, a team of biochemists conducted a study designed to explore the usage of optimal codons within genes and their relationship to protein folding. This research looked for correlations between codon usage and a number of parameters in a massive database of DNA sequences from a wide range of representative organisms, including the bacterium, E. coli; the yeast, S. cerevisiae; the nematode, C. elegans; the fruit fly, D. melangaster; the mouse, M. musculus; and humans.

The researchers discovered that critical amino acids tend to be specified by optimal codons. This makes sense, because errors in these positions will be much more detrimental than other positions in the protein chain. Mistakes in these positions are also much more likely to alter protein folding.

They also determined that proteins produced at relatively high levels in the cell have a greater fraction of optimal codons than proteins that occur at low levels. Again, this reflects an elegant strategy. The more often a protein is produced the more opportunity exists for protein misfolding to happen.

The biochemists also identified tissue dependence for the distribution of optimal codons. Tissues comprised of cells that are long-lived with a low turnover rate (like neurons) have proteins encoded by genes with a high fraction of optimal codons compared to rapidly replaced cell types. This again displays a remarkable biological logic. These types of cells would be susceptible to the accumulation of protein aggregates built up over the course of an organism’s life time. The increase of protein aggregates would not be much of an issue for short-lived cells with a high turnover rate.

One final note: The workers found these correlations in the data for all six organisms, suggesting that they have uncovered a universal pattern among all life-forms.

The bottom line: It looks as if the usage of optimal codons is optimized and appears to be undergirded by an impeccable biochemical rationale.

The Implications

Systems and objects produced by human designers are optimized. Optimization in an engineered system requires extensive planning and forethought and, therefore, stands as a hallmark of intelligent design. In fact, optimization is often synonymous with superior design.

As I describe in The Cell’s Design, life scientists have discovered that, like human designs, many biochemical systems are optimized according to a purpose. The usage of optimal codons marks just one more example.

The optimality of biochemical systems far exceeds the accomplishments of the finest human engineers and designers, in a way befitting a supernatural Creator. Biochemical optimization indicates that life must have materialized from the Divine Artist’s hand.

Biochemical design: It’s the real thing.