How Complex Is Life?

As the human genome project’s influence grows, one of the concepts that has emerged is complexity. Scientists including biologists have appreciated for some time that genetic networks drive development and biological responses. The cell’s responses to stimuli require and ever changing cast of proteins. The instructions for the protein sequences are encoded within the genome. If we could understand how this large cast of proteins is assembled into smaller pathways and responses we would be considerably further along. The parts list is long and complex, but as the genome project began to uncover the instructions for how the “parts” are made there was a feeling that science may be able to build models that describe function and disease.

The 2010 Nature article describes this aspiration:

The hope was that by cataloguing all the interactions in the p53 network, or in a cell, or between a group of cells, then plugging them into a computational model, biologists would glean insights about how biological systems behaved

And indeed this did (and still does) seem like a reasonable approach. Biological networks have turned out to be as complex as we could have hoped. Systems biology is still moving forward, but the sheer number of possible rules that govern how all of the cellular parts work together and interact suggest that we will be working with this complexity for some time. There is a universe of rules that describe networks; explaining how proteins, ligands, nucleic acids and more interact and result in function.

Towards the end of the article there is an interesting quote from Bert Vogelstein:

“Humans are really good at being able to take a bit of knowledge and use it to great advantage,”

And we are. With some careful science and good detective skills we can take what we do know and put it to good use, combating disease. The fact that biological systems are complex and that this complexity is not simply going to be understood the first time we draw back the curtain is a great finding.

I am asking the Tox1401 students to look into this complexity a bit further. Let’s start with a pathway database like reactome.org. Choose the phase II pathways and select a single protein within that pathway, perhaps the NAT1 arylamine N-acetyltransferase. Provide a description of the protein, and the pathway that it takes part in.

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32 thoughts on “How Complex Is Life?

  1. The protein I selected is CYPIA2, which is located in the endoplasmic reticulum membrane. It is involved in a methylation pathway, specifically the S-atom dealkylation of 6-methylmercaptopurine. 6-methylmercaptopurine, which is found in the endoplasmic reticulum lumen reacts with O2 and H+ and uses up NADPH. CYPIA2 then catalyzes the reaction to form 6-mercaptopurine, producing H2O and formaldehyde as byproducts and converting NADPH to NADP+.
    CYPIA2 is an enzyme and has been found to be linked to addiction to caffeine. It breaks down the caffeine in the liver, and those born with a more active form of the CYPIA2 gene break down caffeine more quickly, requiring more caffeine throughout the day to keep them going. CYPIA2 is in a family of 450 cytochromes that are linked to metabolism.

    • If people who born with more CYPIA2 proteins break down caffeine quickly as caffeine is metabolized by CYP1A2 in the liver, does it necessarily mean that high level of CYPIA2 gene expression will boost one’s metabolism?

      • High levels of CYP1A2 will break down the caffeine. How can it boost up the metabolism if the protein CYP1A2 is constantly degrading it? Is there sufficient time for it to process and cause a response?

  2. I chose the Glycine-N-AcylTransferase protein that is located in the mitochondria matrix. A shorter name for this protein is GLYAT, from my understanding it is an amino acid conjugation located in humans and its function is to transfer mitochondria primarily in the liver or kidney, that then transfers to an acyl group to glycine. It is also able to multiply the substrates to form more N-acylglycines. The role that this protein plays is detoxing xenobiotics within the carboxylic group which is shown within the diagram. Xenobiotics are chemicals found in the human body aka the fatty acids, or things that our body does not produce naturally and we humans produce them artificially.

    • GLYAT is more involved in organic acid metabolism such as conjugation of benzoic acid and salicyclic acid. You’re correct in saying that the function is to detoxify acids by transferring acyl groups to glycine.

  3. NAT2, or arylamine N-acetyltransferase, is a type of protein that encodes an enzyme, N-acetyltransferase, in order to both activate and deactivate arylamine and hydrazine drugs and bladder carcinogens. This type of protein can be found in cytosol and is located near to NAT1. And it takes place during the acetylation pathway, NAT2 acetylation in particular. As NAT2 primarily participates in the detoxification of aromatic monoamines (PubMed), it is expressed in the liver and might increase the risk of having bladder cancer in humans. Prostate cancer in males due to NAT2 slow acetylation, which is caused by certain allelic recombination, is also very common.

    • If prostate cancer in males due to slow acetylation is something very common, are there any steps that can be taken in order to increase the rate of acetylation? Since prostate cancer occurs often, i’m just curious to know if there’s anything that has been done to resolve the issue.

    • (NATs) are involved in the metabolism of a variety of different compounds that we are exposed to on a daily basis. The levels of NATs in the body have important consequences with regard to an individual’s susceptibility to certain drug-induced toxicities and cancers.

  4. In regards to the Phase II conjugation pathway, I have chosen the protein Nicotinamide N-Methyltransferase, also referred to as NNMT. Nicotinamide N-Methyltransferase is an S-adenosyl-L-methionine dependent enzyme that catalyzes the N-Methylation of nicotinamine and other pyridines. It is approximately 16.5 Kb and consists of 3 exons and 2 introns. NNMT is considered to be part of the methylation pathway. N-Methylation is one method by which drugs and other xenobiotics are metabolized by the liver. Nicotinamide N-Methyltransferase is mainly expressed in the liver; however there has been the detection of expression in the kidneys, lung, brain, and heart. The abnormal expression of NNMT has been identified in several tumors such as bladder cancer and stomach adenocarcinoma.

    • Is there a way to inhibit the NNMT protein to prevent the cells from proliferating and developing into bladder cancer and stomach adenocarcinoma?

  5. Glycine N-Acyltransferase, or GLYAT, is located within the mitochondria and is involved in phase II conjugation. It functions in transferring acetyl groups from xenobiotic compounds, usually benzoic acid and salicyclic acid. GLYAT is located in the mitochondria and uses acyl-CoA as a substrate for its conjugation reactions. The highest expression levels of GLYAT are found in the liver and kidneys, where the detoxification of xenobiotics and endogeneous metabolites is a high priority. Those with nonfunctional GLYAT have various complications that come with defective organic acid metabolism.

    • You do a great job explaining where GLYAT is located and how it is structured. You did not mention what the purpose of GLYAT is, how does it effect the body in both positive and negative ways? You mention that this protein functions in transferring acetyl groups from xenobiotic compounds like salicylic acid, you could build on this to explain what the body’s reaction to this is.

  6. For my protein, I chose Nicotinamide N-methyltransferase, which is located in the cytosol of the cell. It is part of the metabolic pathway and takes part in nicotinate and nicotinamide metabolism. The enzyme is found in humans, mice, and rats. In humans, it helps with tumor differentiation when dealing with oral squamous cell carcinoma, the most common oral or pharyngeal cancer, and it is also related to cell migration. It can help with the cancer because it can be used as a tumor marker depending on the substrate it is bound to. Nicotinamide N-methyltransferase is in the transferase family, especially those that transferone-carbon group methyltransferases. Transferases help catalyze the transfer of a functional group.

    • This is hopefully the next step to dealing and identifying oral cancer. If this enzyme is found in humans and rats does I think it would be especially helpful so mice and rats can undergo research to efficiently identify a tumor-seeking technique for humans. If a protein we already produce naturally can help differentiate between tumors we, as scientists may have to look no further for developing new techniques.

  7. SULT1A1
    Under Phase II conjugation there are many reactions that take place simply put there are 6 categories of reactions in which delve into a much more complicated network of reactions. Glucronidataion, Sulfonation, Acetylation, Methylation, Glutathion conjugation and Amino Acid conjugation. Specifically, I chose the sulfotransferase activity in which Acetaminophen can form an O-sulfate conjugate which lies under Phase II sulfonation. Sulfotransferase activity is the catalysis of the transfer of a sulfate group from 3′-phosphoadenosine 5′-phosphosulfate to the hydroxyl group of an acceptor, producing the sulfated derivative and 3′-phosphoadenosine 5′-phosphate.This reaction takes place in the cytosol and is mediated by the ‘aryl sulfotransferase activity’ of SULT1A1 homodimer. This direct correlation of the intake of acetaminophen and sulfonation metabolites have been extensively studied. SULT1A1 catalyzes the sulfate conjugation of not only acetaminophen rather of a broader variety such as catecholamines, phenolic drugs and neurotransmitters. Is also responsible for the sulfation and activation of minoxidil. Interestingly enough, it mediates the metabolic activation of carcinogenic N-hydroxyarylamines to DNA binding products and could so participate as modulating factor of cancer risk.

  8. Thiopurine S-methyltransferase is a protein found in humans, containing 9 stranded core beta sheets, in between two sets of alpha helices. Its job is to metabolize thiopurine drugs, which are usually used to treat leukemia and other autoimmune disorders. If there is a defect in the thiopurine s-methyltransferase this could lead to enhanced bone marrow toxicity which may cause myelosuppression, anemia, bleeding tendency, leukopenia and infection, due to enhanced bone marrow toxicity. Therefore without this protein, or with a deficiency of this protein, are at high risk for bone marrow toxicity. This protein is currently being researched, due to its advancement in the treatment of Chron’s disease.

    • Chrons disease is a form of intestinal disease so it makes sense that a metabolic protien such as this one can help regulation. In Chrons disease there is a sensitivity similar to that in people With IBS but of greater severity. if this could be safely combined with some way to momentarily make bone marrow more basic to allow the added acidity to create a natural regular flow of pH over the marrow may allow for a shift in these metabolic proteins and allow the enzymes to “calm” down the disorder and prevent further self infliction

  9. Protein Nicotinamide N-methyltransferase (NNMT) located in the cytosol of the cell. It is an S-adenosl-L-methionine and it is a dependent enzyme, which catalyzes NNMT as well as other pyrideines, the enzyme is found in humans, mice and rats. It is a part of the metabolic pathway; drugs and other xenobiotics are metabolized by the liver using NNMT, however, it is also seen in kidneys, lungs, brain and heart but mainly it works in liver. NNMT is used tumor marker and helps differentiate in tumors, other sorts of abnormal expression of NNMT in tumor are seen as bladder cancer and stomach adenocarcinoma. NNMT is considered a Phase II conjugation pathway and has 3 exons and 2 introns and is a part of methylation pathway.

    • These are some really good points. Hopefully with further research on this protein, we can move ahead in cancer research since this protein is used as a tumor marker. You should also add how NNMT metabolized drugs and other xenobiotics.

  10. Catechol-O-methyltransferase takes place in phase 2. COMT is located in the extracellular matrix primarily the plasma membrane. It is involved in the metabolism of catelcholamines and catechol drugs. Dopamine is a catechol drug. Catechol O- methyl transferase donates methyl group from S- adenosylmethionine to acceptor hydroxyl groups on catechol structures. Norephinephrine and Epinephrine is methylated by producing normetanephrine and metanephrine. Parkinson patients are prescribed L-Dopa, in addition they also take Cathechol-O- methyltransferase to prohibits the metabolism of L-Dopa by Catehchol- O- methyltransferase. In the brain COMT degrades neurotransmitters. COMT is vital in the prefrontal cortex which coordinates functions from other areas of the brain. If a deletion of the COMT gene occurs, there is a risk of schizophrenia, depression, anxiety and bipolar disorder. Research is still being conducted to understand the relationship of COMT and disorders.

    • I was confused at first as to why the person would get prescribed COMT when it degrades neurotransmitters, but then after reading further I understand that it can cause multiple disorders. I think that it is wierd that they are prescribed something that would cause their neurotransmitters to degrade, yet if you live without it, or with little of it, then you can become bipolar or obtain anxiety.

    • Good points. Is there a linkage to schizophrenia and Parkinson disease being hereditary is there any genetic or chromosomal effects that take place leading to offspring being the carrier or at a potential risk for the disease.

    • I also read that two versions of enzymes are made from this gene; MB-COMT which is produced by nerve cells in the brain and S-COMT that helps control the levels of certain hormones. In COMT genes some researchers have found a slightly increased risk of schizophrenia in people with valine at position 108/158.

  11. Among many of the proteins found in the cytosol bisphosphate 3′-nucleotidase 1 (BPNT1) is a member of a magnesium dependent family known as phosphomonoesterase. These proteins specialize as metabolic intermediates that oversee production of mainly inhibitors for allosteric regulation, barley effecting cell function if there is any “noticed”. These receptors are being utilized as targets for medicines to allow a more proper flow of these enzymes to help catalyze reactions properly. Currently in use with the alleviation of manic depression. The actual protien itself seems to deal with the regulation over our metabolisms access to sulfur. Starting with PhosphAte PhosphoSulfate (PAPS) to Adenosine PhosphoSulfate (APS) and
    PhosphoAdenosine Phosphate (PAP) to Adenosine MonoPhosphate (AMP) that can be on its way to phophorilization and become Adenosine TriPhosphate (ATP). This might explain the fatigue and tiredness brought on by depression as lower values of AMP inhibbit ATP (energy) production
    –Information is mainly from the Weizmann Institute of Science website genecards.org

    • The BPNT1 gene found in mice or rats has been deemed around 90% similar to that of the Human corresponding gene

    • Hey I also wanted to add that BPNT is expressed in highest levels in brain and kidney as well and this drug is also used for the treatment bipolar affective disorder, etiology of mood disorders.

  12. CYPIA2 is a gene that is involved in drug metabolism. Found in the liver it is characterized to give a somewhat weaker effect that CYPIA1. In an experiment conducting using 7 ethoxyresorufin as a substrate testing the metabolism of caffeine, and multiple phenoxazone ethers there was a remarkable production of both CYPIA1 and CYPIA2.
    CYPIA2 is produced by the liver during the metabolism of certain drugs and it is dna specific according to research done by the pharmacology department of the university of California. CYPIA2 is stored as a protein in the endoplasmic reticulum which function as a storage molecule inside the cell.

  13. Glycine-N-AcylTransferase, or GLYAT, is a protein located in the mitochondrial matrix and it is involved in phase II conjugation. It is an enzyme that transfers acetyl groups from xenobiotic compounds. A xenobiotic is a chemical that is found in an organism that is normally not produced or expected to be present in. The two main substrates for this enzyme is acyl-CoA and glycine and the two main products are CoA and N-acylglycine. The common xenobiotic compounds GLYAT function mainly on are benzoic acid and salicyclic acid. GLYAT are highly expressed in the liver and kidney. The conjugation of a carboxylic acid xenobiotic with an amino acid happens before excretion.

      • You made some really good points and did a great job in describing GLYAT. However, what is the purpose of GLYAT in the body and what positive/negative effects can it have?

  14. Nicotinamide N-methyltransferase, or NNMT, is and enzyme that is encoded by the NNMT gene in humans. NNMT is located on the in the cytosol of the cell and involved in the phase II conjugation pathway. NNMT catalyzes the N-methylation of nicotinamide and other pyridines to form pryidinium ions. N-methylation is one method by which drugs and other xenobiotic compounds are metabolized by the liver. NNMT is mainly expressed in the liver. However, NNMT has also been detected in the kidneys, lungs, brain, and heart. The NNMT gene is located on chromosome 11. The NNMT gene is approximately 16.5 KB in length and consists of three exons and two introns. In addition, this gene encodes the protein responsible for this enzymatic activity, N-methylation, which uses S-adenosly methionine as the methyl donor. The N-methylation of nicotinamide is altered in some diseases including Parkinson’s disease, hepatic cirrhosis, chronic obstructive pulmonary disease (COPD), and atherosclerosis. In addition, the abnormal expression of NNMT has been identified in several kinds of tumors. Examples of these include glioblastoma, stomach adenocarcinoma, papillary thyroid cancers, renal carcinoma, oral squamous carcinoma, colorectal cancer, hepatocellular carcinoma, bladder cancer, lung cancer, and pancreatic cancer. NNMT can also be used as a tumor marker.

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