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Does the mutation CCR5-delta 32 increase the genetic info?

Does the mutation CCR5-delta 32 increase the genetic info?


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My understanding is that the mutation CCR5-delta 32 caused the CCR5 co-receptor to be of a different shape, resulting HIV virus to not be able to attach itself to it.

My question, this shape/mutation, is it a result of a more or less information in the genetic information of the person with the mutation as compared to one without it?


Whether or not a mutation changes the 'amount' (meaning the size of the genome) of genetic information present in an individual depends on the type of mutation and is independent on which gene is affected.

In general there are 3 types of mutations:

  • point mutation: this is the change of one base pair to another (e.g. A to C). The total amount of information/the size of the genome is unchanged.
  • deletion: this means that a certain stretch of DNA is missing, likely disrupting what was there before. The total amount of information/the size of the genome is reduced.
  • insertion: this means additional DNA was added at a certain place in the DNA and probably disrupts something that was there before. The total amount of information/the size of the genome is increased.

The CCR5-delta32 mutation is caused by the deletion of a few (only 32) base pairs, however this deletion causes a frame shift in the gene and therefore leads to an early stop codon, which renders the protein inactive.


A Scientist Edited Babies' Genes In Utero. It Could Make Them More Likely to Die Early.

UPDATE: On Oct. 8, the journal Nature Medicine retracted the paper described in the article below due to crucial errors in the analysis. The errors invalidate the conclusion that the first gene-edited babies could have shorter life spans. Live Science published the original article (below) on June 3.

When a Chinese scientist announced last year that he had used CRISPR technology to edit the genomes of twin babies in an attempt to make them resistant to HIV infection, the move was decried as both unethical and potentially harmful to the babies.

Now, a new study underscores some of these concerns: The results suggest that the genetic mutation that was attempted in the CRISPR babies is tied to an increased risk of early death.

Specifically, the study found that this mutation &mdash which is known as CCR5-delta 32 and which occurs naturally in a small percentage of people &mdash is tied to a 20% increase in the risk of death before age 76. [9 Absolutely Evil Medical Experiments]

"Beyond the many ethical issues involved with the CRISPR babies … it is still very dangerous to try to introduce mutations without knowing the full effect of what those mutations do," study senior author Rasmus Nielsen, a professor of integrative biology at the University of California, Berkeley, said in a statement. In the case of the CCR5-delta 32 mutation, "it is probably not a mutation that most people would want to have. You are actually, on average, worse off having it."


Mutation that Protects Against HIV Infection May Raise Risk of West Nile Virus Illness

People who lack a cell surface protein called CCR5 are highly resistant to infection by HIV but may be at increased risk of developing West Nile virus (WNV) illness when exposed to the mosquito-borne virus, report researchers from the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH). The study, by Philip M. Murphy, M.D., and colleagues, appears online today in The Journal of Experimental Medicine. The findings may have cautionary implications for physicians who are treating HIV-positive individuals with experimental CCR5-blocking drugs, say the scientists.

“This is the first genetic risk factor to be identified for West Nile virus infection,” says NIH Director Elias A. Zerhouni, M.D. “While infection does not always lead to illness, the virus can sometimes cause serious problems and, according to the Centers for Disease Control and Prevention, there were 102 deaths in the United States from West Nile virus infection in 2005.”

“A decade ago, a number of research groups, including Dr. Murphy’s, determined that CCR5 is the primary co-receptor used by HIV to infect cells,” says NIAID Director Anthony S. Fauci, M.D. “Their work laid the foundation for the development of CCR5-blocking drugs, which are designed to slow the spread of HIV from cell to cell.”

Most people inherit two normal copies (one from each parent) of the gene that codes for CCR5 protein. About 1 percent of North American whites, however, have a mutation in both copies (are homozygous) and thus do not produce any CCR5. These individuals have the good fortune of being highly resistant to HIV infection and otherwise seemed to suffer no ill effects from the absence of this receptor protein, scientists noted. But the new research by Dr. Murphy’s team suggests that lacking CCR5 may not be an unalloyed good after all.

In 2005 Dr. Murphy and his coworkers developed a mouse model to clarify the roles of various immune system cells in responding to WNV infection. They discovered that while most wild-type mice survived WNV infection, mice genetically engineered to lack CCR5 receptors suffered rapid and uniformly fatal infection by the virus. Further investigation showed that CCR5 promoted the movement of several classes of immune system cells into the brain and central nervous system, which appeared to protect normal mice from the encephalitis (brain inflammation) characteristic of serious WNV infection.

“We wanted to know if humans lacking CCR5 might be at greater risk of the more serious complications of WNV infection,” says Dr. Murphy. The researchers examined human blood and cerebrospinal fluid samples from 417 laboratory-confirmed cases of WNV infection that occurred in Arizona and Colorado in 2003 and 2004. Of these, 395 were suitable for genetic testing for the presence or absence of the HIV-protective mutation.

Dr. Murphy and his colleagues determined that 4.5 percent of 247 WNV-positive samples from Arizona were from patients who had two copies of the CCR5 mutation. In contrast, a control group of 145 WNV-negative blood samples showed 0.7 percent were from people who had two copies of the CCR5 mutation — a number in line with the expected 0.8 to 1 percent range believed to be present in all North American whites. Next, the researchers analyzed the WNV-positive samples from Colorado and determined that 4.1 percent of the entire set of 148 samples came from individuals homozygous for the CCR5 mutation. Among those Coloradans who provided WNV-positive samples and who self-reported their race as white, the percentage of homozygous individuals was 8.3.

The absence of normal CCR5 genes is a strong genetic risk factor for developing symptomatic cases of WNV infection, the researchers conclude. “The findings may have important clinical implications for physicians who treat people with HIV,” notes Dr. Murphy. For example, he says, it may be prudent for HIV-positive individuals who are taking experimental CCR5-blockers to strictly limit mosquito exposure.


Biologists discover why 10% of Europeans are safe from HIV infection

Scientists have known for some time that these individuals carry a genetic mutation (known as CCR5-䲰) that prevents the virus from entering the cells of the immune system but have been unable to account for the high levels of the gene in Scandinavia and relatively low levels in areas bordering the Mediterranean.

They have also been puzzled by the fact that HIV emerged only recently and could not have played a role in raising the frequency of the mutation to the high levels found in some Europeans today.

Professor Christopher Duncan and Dr Susan Scott from the University's School of Biological Sciences, whose research is published in the March edition of Journal of Medical Genetics, attribute the frequency of the CCR5-䲰 mutation to its protection from another deadly viral disease, acting over a sustained period in bygone historic times.

Some scientists have suggested this disease could have been smallpox or even bubonic plague but bubonic plague is a bacterial disease rather than a virus and is not blocked by the CCR5-䲰 mutation.

Professor Duncan commented: "The fact that the CCR5-䲰 mutation is restricted to Europe suggests that the plagues of the Middle Ages played a big part in raising the frequency of the mutation. These plagues were also confined to Europe, persisted for more than 300 years and had a 100% case mortality."

Around 1900, historians spread the idea that the plagues of Europe were not a directly infectious disease but were outbreaks of bubonic plague, overturning an accepted belief that had stood for 550 years. Professor Duncan and Dr Scott illustrated in their book, Return of the Black Death (2004, Wiley), that this idea was incorrect and the plagues of Europe (1347-1660) were in fact a continuing series of epidemics of a lethal, viral, haemorrhagic fever that used the CCR5 as an entry port into the immune system. Using computer modeling, they demonstrated how this disease provided the selection pressure that forced up the frequency of the mutation from 1 in 20,000 at the time of the Black Death to values today of 1 in 10.

Lethal, viral haemorrhagic fevers were recorded in the Nile valley from 1500 BC and were followed by the plagues of Mesopotamia (700-450BC), the plague of Athens (430BC), the plague of Justinian (AD541-700) and the plagues of the early Islamic empire (AD627-744). These continuing epidemics slowly raised the frequency from the original single mutation to about 1 in 20,000 in the 14th century simply by conferring protection from an otherwise certain death.

Professor Duncan added: "Haemorrhagic plague did not disappear after the Great Plague of London in 1665-66 but continued in Sweden, Copenhagen, Russia, Poland and Hungary until 1800. This maintenance of haemorrhagic plague provided continuing selection pressure on the CCR5-䲰 mutation and explains why it occurs today at its highest frequency in Scandinavia and Russia."

The University of Liverpool is one of the UK's leading research institutions with a prodigious spread of expertise - from the humanities and social sciences to engineering, science, veterinary science and medicine. It attracts collaborative and contract research commissions from a wide range of national and international organisations - commissions valued at more than £80 million annually.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.


40 POINTS! PLEASE HELP!

1. what Genotype would result in a yellow coat phenotype?

2. what is the phenotype of A?

3. what is the result of the process called crossing over?

a. Deletion of amino acids in offspring

b. production of gametes in offspring

c. genotype difference of offspring

d. increase in a mutation of offspring

4. The only cells that contribute to an offspring genotype are? choose all that apply.

5. What type of mutation occurred in mutant 3?

6. What type of mutation occurred in mutant 2?

7. According to Nature. com, "A genetic mutation known as CCR5-delta 32 is responsible for the two types of HIV resistance that exist. CCR5-delta 32 hampers HIV's ability to infiltrate immune cells. The mutation causes the CCR5 co-receptor on the outside of cells to develop smaller than usual and no longer sit outside of the cell." Which statement explains how these mutations occur?

a. A mutation occurs when HIV enters the cell

b. A mutation occurs when nucleic acids are replicated

c. A mutation occurs during mitosis

8. A female, heterozygous for dark hair and freckles married a male homozygous dominant for dark hair and he has no freckles. What % of their offspring will have dark hair and freckles?

9. A farmer wants to use the young plants that came from his P1 & P2 cross. He did gel electrophoresis his plants to determine which ones were related to his P1 and P2. Which plants should he not choose? answer for no choose all that apply.

10. the central dogma states: the genes on DNA gets _ into ___, which get _ into a _.

a. translated: Rna: transcribed: protein

b. Transcribed: RNA: translated: protein

c. Translated: DNA: Transcribed: RNA

d. Transcribed:DNA: translated: RNA

11. If the allele for tall pea plants (T) is dominant over the allele for short pea plants (t) what is the genotype of a homozygous tall pea plant?

12. using the info from the question above, what percent of the offspring would be short if one parent is homozygous dominant, and the other is heterozygous?

13.which molecule was coded for by the longest piece of DNA, assuming no post-transcriptional RNA processing or splicing has occurred?


Addendum August 2007

&lsquoA new generation of sophisticated therapies designed to HIV-proof the immune system promises to enter the clinic soon. For example, [Carl] June, working with Sangamo Bio-Sciences in Richmond, California, later this year plans to start trials in 12 HIV-infected people of a gene therapy designed to endow immune cells with a genetic mutation that protects them from HIV.

To infect immune cells, HIV must first bind to chemokine receptors. Researchers discovered in 1996 that people who had a naturally occurring mutation in their genes for one of these, CCR5, were strongly protected from developing AIDS&mdashor even becoming infected in the first place&mdashand suffered no ill effects from lacking the receptor.

Sangamo specializes in developing enzymes called zinc finger nucleases that can bind to genes, clip their DNA, and repair mutations (Science, 23 December 2005, p. 1894). But for the HIV gene therapy, they&rsquove created a nuclease to specifically disrupt the CCR5 gene in the same manner as the natural mutation. In the new trial, researchers will put the gene for this zinc finger nuclease into an adenovirus vector, transduce harvested CD4 + T cells of HIV-infected people, and infuse those cells back. June says this is the first gene-therapy experiment that aims to create a phenotype that&rsquos known to confer disease resistance.&rsquo 26


Multiple Choice

Which of the following is a change in the sequence that leads to formation of a stop codon?

A. missense mutation
B. nonsense mutation
C. silent mutation
D. deletion mutation

The formation of pyrimidine dimers results from which of the following?

A. spontaneous errors by DNA polymerase
B. exposure to gamma radiation
C. exposure to ultraviolet radiation
D. exposure to intercalating agents

Which of the following is an example of a frameshift mutation?

A. a deletion of a codon
B. missense mutation
C. silent mutation
D. deletion of one nucleotide

Which of the following is the type of DNA repair in which thymine dimers are directly broken down by the enzyme photolyase?

A. direct repair
B. nucleotide excision repair
C. mismatch repair
D. proofreading

Which of the following regarding the Ames test is true?

A. It is used to identify newly formed auxotrophic mutants.
B. It is used to identify mutants with restored biosynthetic activity.
C. It is used to identify spontaneous mutants.
D. It is used to identify mutants lacking photoreactivation activity.


CRISPR gene editing can create cells immune to HIV

CRISPR gene editing was safe and moderately effective in introducing stem cells that lacked the CCR5 receptor and were immune to HIV infection after chemotherapy eradicated the immune system of a man with HIV and acute lymphocytic leukaemia, Chinese researchers report in The New England Journal of Medicine this week.

The CCR5 receptor on human cells is used by HIV to gain entry to the cell. When the CCR5 receptor is not present on the cell surface, HIV cannot gain entry to the cell unless it has evolved to use another receptor, CCR4. Most viruses are not adapted to use CCR4. A genetic mutation called CCR5-delta 32 prevents HIV infection entirely if a person inherits the mutation from both parents. Around 1% of people of northern European descent are CCR5-delta 32 homozygous, meaning they have inherited the mutation from both parents.

The Chinese experiment was designed to test whether it was possible to genetically engineer an equivalent to the eradication of HIV in Timothy Ray Brown. The so-called 'Berlin patient' appears to have been cured of HIV after a stem cell transplant from a donor lacking the CCR5 receptor repopulated his immune system after chemotherapy to treat acute myeloid leukaemia.

Glossary

A protein on the surface of certain immune system cells, including CD4 cells. CCR5 can act as a co-receptor (a second receptor binding site) for HIV when the virus enters a host cell. A CCR5 inhibitor is an antiretroviral medication that blocks the CCR5 co-receptor and prevents HIV from entering the cell.

Cells from which all blood cells derive. Bone marrow is rich in stem cells.

A unit of heredity, that determines a specific feature of the shape of a living organism. This genetic element is a sequence of DNA (or RNA, for viruses), located in a very specific place (locus) of a chromosome.

In cell biology, a structure on the surface of a cell (or inside a cell) that selectively receives and binds to a specific substance. There are many receptors. CD4 T cells are called that way because they have a protein called CD4 on their surface. Before entering (infecting) a CD4 T cell (that will become a “host” cell), HIV binds to the CD4 receptor and its coreceptor.

The material in the nucleus of a cell where genetic information is stored.

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein 9. It is a gene-editing technique by which researchers can design a piece of RNA to attach to a specific site in a DNA chain. The RNA is packaged with a bacterial enzyme, Cas9, which cuts DNA. The cell’s own genetic repair machinery then inserts a customised sequence of DNA.

In the case of CRISPR gene editing for CCR5 deletion, the technique introduces a DNA sequence that contains the code to make new stem cells or progenitor cells that lack the CCR5 receptor. These blood stem and progenitor cells will differentiate into a wide range of blood cells that include CD4+ and CD8+ lymphocytes. All the progeny of these stem cells will lack the CCR5 receptor.

No results from trials of CRISPR-based therapies for any disease have been published yet, so the Chinese results are amongst the first to report on the safety of the technique. Chinese researchers are at the forefront of CRISPR-based therapeutic research in cancer.

A Chinese scientist claimed earlier this year to have used CRIPSR to genetically engineer immunity to HIV infection by embryonic genome editing, so that twin girls were born CCR5-homozygous. That experiment was strongly condemned as unethical by other researchers and human embryo genome editing is prohibited in many countries except for laboratory research.

Professor Hongkui Deng of Peking University Stem Cell Research Center and colleagues at major research institutions in Beijing reported on the case in The New England Journal of Medicine. He was not associated with the CRISPR editing experiments on human embryos.

This experiment tested the safety and feasibility of transplantation of CRISPR-Cas9-modified stem cells into a person living with HIV during treatment for acute lymphocytic leukaemia. The person studied was a 27-year-old man, diagnosed with HIV two weeks prior to a diagnosis of acute lymphocytic leukaemia in 2016. At diagnosis he had a CD4 cell count of 528 cells/mm3 and a viral load of 850,000 copies/ml (a viral load suggestive of primary infection, a question not addressed by the study authors). He started antiretroviral treatment immediately and achieved an undetectable viral load one year later. He received six courses of chemotherapy and achieved complete remission of leukaemia. In June 2017 he underwent a stem cell transplant from a donor who had unmutated CCR5 gene. The stem cell transplant is a routine procedure after chemotherapy for acute lymphocytic leukaemia.

Before transplantation, CD34+ cells were harvested and subjected to CRISPR editing in order to insert the CCR5 gene mutation.

Of the cells harvested, 17% were gene-edited. After engraftment, CCR5-deleted cells never comprised more than 5-8% of the karyocytes in the bone marrow (precursors for white blood cells). Cells descended from the engrafted cells showed similar proportion of CCR5-deleted cells, showing that the edited gene persists when the cells differentiate into new types of blood cell. However, a lower proportion of CCR5-deleted cells was found in CD4+ and CD8+ T-cells, perhaps due to the persistence of donor T-cells that were not altered. The CCR5-deleted cells persisted for at least 19 months after transplant.

The patient suffered the usual side-effects of a stem cell transplant including anaemia, neutropenia and thrombocytopenia, but no adverse effects of CCR5 deletion were detected. No gene-edits away from the target site in the genome were detected in cells sampled from bone marrow four months, 12 months and 19 months after transplantation.

However, in an accompanying editorial Professor Carl June of the University of Pennsylvania’s Center for Cellular Immunotherapies warns that the low frequency of CCR5-deleted cells and the consequent small sample in a single patient means that rare genetic changes might be missed.

Seven months after transplantation an analytic treatment interruption took place to determine if the CCR5-deleted cells had any impact on viral load. The patient provided written informed consent for the treatment interruption. By this time his CD4 count had normalised to over 500 cells/mm3, having declined to around 200 cells/mm3 150 days after transplantation, and he had an undetectable viral load.

The treatment interruption lasted four weeks, during which time the patient’s viral load increased to 3 million copies/ml and his CD4 cell count declined to 250 cells/mm3. The study protocol required treatment to be resumed if viral load exceeded 100,000 copies/ml or the CD4 cell count fell below 250 cells/mm3. Viral load became undetectable again after treatment was resumed.

Levels of total and integrated HIV-1 DNA in CD4 cells increased after treatment interruption by approximately 2 log, indicating rapid expansion of the HIV reservoir, and still remained above the pre-interruption level a year later.

During the treatment interruption the proportion of CCR5-deleted CD4+ T-cells increased from 2.96% to 4.39%.

Find out more: The search for an HIV cure

“To further clarify the anti-HIV effect of CCR5-ablated HSPCs, it will be essential to increase the gene-editing efficiency of our CRISPR-Cas9 system and improve the transplantation protocol,” the researchers conclude. Alteration of more cells in a donor sample and the engraftment of a higher proportion of the altered cells might lead to a larger population of CCR5-deleted cells in the recipient. So might engineering of pluripotent stem cells, which are the precursors to blood stem cells.

The researchers point out that CRISPR-Cas9 editing of blood stem cells may overcome a potential drawback of the CCR5 delta-32 mutation – reduced life expectancy, as identified in a recently published study – by only editing blood cells. The mechanism by which CCR5 might affect life expectancy remains unclear, although some scientists argue that the mutation might increase vulnerability to some viral infections such as influenza.

Lei Xu et al. CRISPR-edited stem cells in a patient with HIV and acute lymphocytic leukemia. The New England Journal of Medicine, advance online publication, 11 September 2019. DOI: 10.1056/NEJMoa1817426

June CH. Emerging use of CRISPR technology – chasing the elusive HIV cure. The New England Journal of Medicine, advance online publication, 11 September 2019. DOI: 10.1056/NEJMe1910754


6.5: Mutations

  • Contributed by OpenStax
  • General Biology at OpenStax CNX
  • Compare point mutations and frameshift mutations
  • Describe the differences between missense, nonsense, and silent mutations
  • Explain how different mutagens act
  • Compare different types o f repair mechanisms
  • Explain why the Ames test can be used to detect carcinogens
  • Analyze sequences of DNA and identify examples of types of mutations

A mutation is a heritable change in the DNA sequence of an organism. The resulting organism, called a mutant, may have a recognizable change in phenotype compared to the wild type, which is the phenotype most commonly observed in nature. A change in the DNA sequence is conferred to mRNA through transcription, and may lead to an altered amino acid sequence in a protein on translation. Because proteins carry out the vast majority of cellular functions, a change in amino acid sequence in a protein may lead to an altered phenotype for the cell and organism.

Effects of Mutations on DNA Sequence

There are several types of mutations that are classified according to how the DNA molecule is altered. One type, called a point mutation, affects a single base and most commonly occurs when one base is substituted or replaced by another. Mutations also result from the addition of one or more bases, known as an insertion, or the removal of one or more bases, known as a deletion.

What type of a mutation occurs when a gene has two fewer nucleotides in its sequence?

Effects of Mutations on Protein Structure and Function

Point mutations may have a wide range of effects on protein function (Figure (PageIndex<1>)). As a consequence of the degeneracy of the genetic code, a point mutation will commonly result in the same amino acid being incorporated into the resulting polypeptide despite the sequence change. This change would have no effect on the protein&rsquos structure, and is thus called a silent mutation. A missense mutation results in a different amino acid being incorporated into the resulting polypeptide. The effect of a missense mutation depends on how chemically different the new amino acid is from the wild-type amino acid. The location of the changed amino acid within the protein also is important. For example, if the changed amino acid is part of the enzyme&rsquos active site, then the effect of the missense mutation may be significant. Many missense mutations result in proteins that are still functional, at least to some degree. Sometimes the effects of missense mutations may be only apparent under certain environmental conditions such missense mutations are called conditional mutations. Rarely, a missense mutation may be beneficial. Under the right environmental conditions, this type of mutation may give the organism that harbors it a selective advantage. Yet another type of point mutation, called a nonsense mutation, converts a codon encoding an amino acid (a sense codon) into a stop codon (a nonsense codon). Nonsense mutations result in the synthesis of proteins that are shorter than the wild type and typically not functional.

Deletions and insertions also cause various effects. Because codons are triplets of nucleotides, insertions or deletions in groups of three nucleotides may lead to the insertion or deletion of one or more amino acids and may not cause significant effects on the resulting protein&rsquos functionality. However, frameshift mutations, caused by insertions or deletions of a number of nucleotides that are not a multiple of three are extremely problematic because a shift in the reading frame results (Figure (PageIndex<1>)). Because ribosomes read the mRNA in triplet codons, frameshift mutations can change every amino acid after the point of the mutation. The new reading frame may also include a stop codon before the end of the coding sequence. Consequently, proteins made from genes containing frameshift mutations are nearly always nonfunctional.

Figure (PageIndex<1>): Mutations can lead to changes in the protein sequence encoded by the DNA.

  1. What are the reasons a nucleotide change in a gene for a protein might not have any effect on the phenotype of that gene?
  2. Is it possible for an insertion of three nucleotides together after the fifth nucleotide in a protein-coding gene to produce a protein that is shorter than normal? How or how not?

Since the first case of infection with human immunodeficiency virus (HIV) was reported in 1981, nearly 40 million people have died from HIV infection, 1 the virus that causes acquired immune deficiency syndrome (AIDS). The virus targets helper T cells that play a key role in bridging the innate and adaptive immune response, infecting and killing cells normally involved in the body&rsquos response to infection. There is no cure for HIV infection, but many drugs have been developed to slow or block the progression of the virus. Although individuals around the world may be infected, the highest prevalence among people 15&ndash49 years old is in sub-Saharan Africa, where nearly one person in 20 is infected, accounting for greater than 70% of the infections worldwide 2 (Figure (PageIndex<2>)). Unfortunately, this is also a part of the world where prevention strategies and drugs to treat the infection are the most lacking.

Figure (PageIndex<2>): HIV is highly prevalent in sub-Saharan Africa, but its prevalence is quite low in some other parts of the world.

In recent years, scientific interest has been piqued by the discovery of a few individuals from northern Europe who are resistant to HIV infection. In 1998, American geneticist Stephen J. O&rsquoBrien at the National Institutes of Health (NIH) and colleagues published the results of their genetic analysis of more than 4,000 individuals. These indicated that many individuals of Eurasian descent (up to 14% in some ethnic groups) have a deletion mutation, called CCR5-delta 32, in the gene encoding CCR5. CCR5 is a coreceptor found on the surface of T cells that is necessary for many strains of the virus to enter the host cell. The mutation leads to the production of a receptor to which HIV cannot effectively bind and thus blocks viral entry. People homozygous for this mutation have greatly reduced susceptibility to HIV infection, and those who are heterozygous have some protection from infection as well.

It is not clear why people of northern European descent, specifically, carry this mutation, but its prevalence seems to be highest in northern Europe and steadily decreases in populations as one moves south. Research indicates that the mutation has been present since before HIV appeared and may have been selected for in European populations as a result of exposure to the plague or smallpox. This mutation may protect individuals from plague (caused by the bacterium Yersinia pestis) and smallpox (caused by the variola virus) because this receptor may also be involved in these diseases. The age of this mutation is a matter of debate, but estimates suggest it appeared between 1875 years to 225 years ago, and may have been spread from Northern Europe through Viking invasions.

This exciting finding has led to new avenues in HIV research, including looking for drugs to block CCR5 binding to HIV in individuals who lack the mutation. Although DNA testing to determine which individuals carry the CCR5-delta 32 mutation is possible, there are documented cases of individuals homozygous for the mutation contracting HIV. For this reason, DNA testing for the mutation is not widely recommended by public health officials so as not to encourage risky behavior in those who carry the mutation. Nevertheless, inhibiting the binding of HIV to CCR5 continues to be a valid strategy for the development of drug therapies for those infected with HIV.

Causes of Mutations

Mistakes in the process of DNA replication can cause spontaneous mutations to occur. The error rate of DNA polymerase is one incorrect base per billion base pairs replicated. Exposure to mutagens can cause induced mutations, which are various types of chemical agents or radiation (Table (PageIndex<1>)). Exposure to a mutagen can increase the rate of mutation more than 1000-fold. Mutagens are often also carcinogens, agents that cause cancer. However, whereas nearly all carcinogens are mutagenic, not all mutagens are necessarily carcinogens.

Chemical Mutagens

Various types of chemical mutagens interact directly with DNA either by acting as nucleoside analogs or by modifying nucleotide bases. Chemicals called nucleoside analogs are structurally similar to normal nucleotide bases and can be incorporated into DNA during replication (Figure (PageIndex<3>)). These base analogs induce mutations because they often have different base-pairing rules than the bases they replace. Other chemical mutagens can modify normal DNA bases, resulting in different base-pairing rules. For example, nitrous acid deaminates cytosine, converting it to uracil. Uracil then pairs with adenine in a subsequent round of replication, resulting in the conversion of a GC base pair to an AT base pair. Nitrous acid also deaminates adenine to hypoxanthine, which base pairs with cytosine instead of thymine, resulting in the conversion of a TA base pair to a CG base pair.

Figure (PageIndex<3>): (a) 2-aminopurine nucleoside (2AP) structurally is a nucleoside analog to adenine nucleoside, whereas 5-bromouracil (5BU) is a nucleoside analog to thymine nucleoside. 2AP base pairs with C, converting an AT base pair to a GC base pair after several rounds of replication. 5BU pairs with G, converting an AT base pair to a GC base pair after several rounds of replication. (b) Nitrous acid is a different type of chemical mutagen that modifies already existing nucleoside bases like C to produce U, which base pairs with A. This chemical modification, as shown here, results in converting a CG base pair to a TA base pair.

Chemical mutagens known as intercalating agents work differently. These molecules slide between the stacked nitrogenous bases of the DNA double helix, distorting the molecule and creating atypical spacing between nucleotide base pairs (Figure (PageIndex<4>)). As a result, during DNA replication, DNA polymerase may either skip replicating several nucleotides (creating a deletion) or insert extra nucleotides (creating an insertion). Either outcome may lead to a frameshift mutation. Combustion products like polycyclic aromatic hydrocarbons are particularly dangerous intercalating agents that can lead to mutation-caused cancers. The intercalating agents ethidium bromide and acridine orange are commonly used in the laboratory to stain DNA for visualization and are potential mutagens.

Figure (PageIndex<4>): Intercalating agents, such as acridine, introduce atypical spacing between base pairs, resulting in DNA polymerase introducing either a deletion or an insertion, leading to a potential frameshift mutation.

Radiation

Exposure to either ionizing or nonionizing radiation can each induce mutations in DNA, although by different mechanisms. Strong ionizing radiation like X-rays and gamma rays can cause single- and double-stranded breaks in the DNA backbone through the formation of hydroxyl radicals on radiation exposure (Figure (PageIndex<5>)). Ionizing radiation can also modify bases for example, the deamination of cytosine to uracil, analogous to the action of nitrous acid. 3 Ionizing radiation exposure is used to kill microbes to sterilize medical devices and foods, because of its dramatic nonspecific effect in damaging DNA, proteins, and other cellular components.

Nonionizing radiation, like ultraviolet light, is not energetic enough to initiate these types of chemical changes. However, nonionizing radiation can induce dimer formation between two adjacent pyrimidine bases, commonly two thymines, within a nucleotide strand. During thymine dimer formation, the two adjacent thymines become covalently linked and, if left unrepaired, both DNA replication and transcription are stalled at this point. DNA polymerase may proceed and replicate the dimer incorrectly, potentially leading to frameshift or point mutations.

Figure (PageIndex<5>): (a) Ionizing radiation may lead to the formation of single-stranded and double-stranded breaks in the sugar-phosphate backbone of DNA, as well as to the modification of bases (not shown). (b) Nonionizing radiation like ultraviolet light can lead to the formation of thymine dimers, which can stall replication and transcription and introduce frameshift or point mutations.

Table (PageIndex<1>): A Summary of Mutagenic Agents

Mutagenic Agents Mode of Action Effect on DNA Resulting Type of Mutation
Nucleoside analogs
2-aminopurine Is inserted in place of A but base pairs with C Converts AT to GC base pair Point
5-bromouracil Is inserted in place of T but base pairs with G Converts AT to GC base pair Point
Nucleotide-modifying agent
Nitrous oxide Deaminates C to U Converts GC to AT base pair Point
Intercalating agents
Acridine orange, ethidium bromide, polycyclic aromatic hydrocarbons Distorts double helix, creates unusual spacing between nucleotides Introduces small deletions and insertions Frameshift
Ionizing radiation
X-rays, &gamma-rays Forms hydroxyl radicals Causes single- and double-strand DNA breaks Repair mechanisms may introduce mutations
X-rays, &gamma-rays Modifies bases (e.g., deaminating C to U) Converts GC to AT base pair Point
Nonionizing radiation
Ultraviolet Forms pyrimidine (usually thymine) dimers Causes DNA replication errors Frameshift or point

  1. How does a base analog introduce a mutation?
  2. How does an intercalating agent introduce a mutation?
  3. What type of mutagen causes thymine dimers?

DNA Repair

The process of DNA replication is highly accurate, but mistakes can occur spontaneously or be induced by mutagens. Uncorrected mistakes can lead to serious consequences for the phenotype. Cells have developed several repair mechanisms to minimize the number of mutations that persist.

Proofreading

Most of the mistakes introduced during DNA replication are promptly corrected by most DNA polymerases through a function called proofreading. In proofreading, the DNA polymerase reads the newly added base, ensuring that it is complementary to the corresponding base in the template strand before adding the next one. If an incorrect base has been added, the enzyme makes a cut to release the wrong nucleotide and a new base is added.

Mismatch Repair

Some errors introduced during replication are corrected shortly after the replication machinery has moved. This mechanism is called mismatch repair. The enzymes involved in this mechanism recognize the incorrectly added nucleotide, excise it, and replace it with the correct base. One example is the methyl-directed mismatch repair in E. coli. The DNA is hemimethylated. This means that the parental strand is methylated while the newly synthesized daughter strand is not. It takes several minutes before the new strand is methylated. Proteins MutS, MutL, and MutH bind to the hemimethylated site where the incorrect nucleotide is found. MutH cuts the nonmethylated strand (the new strand). An exonuclease removes a portion of the strand (including the incorrect nucleotide). The gap formed is then filled in by DNA pol III and ligase.

Repair of Thymine Dimers

Because the production of thymine dimers is common (many organisms cannot avoid ultraviolet light), mechanisms have evolved to repair these lesions. In nucleotide excision repair (also called dark repair), enzymes remove the pyrimidine dimer and replace it with the correct nucleotides (Figure (PageIndex<6>)). In E. coli, the DNA is scanned by an enzyme complex. If a distortion in the double helix is found that was introduced by the pyrimidine dimer, the enzyme complex cuts the sugar-phosphate backbone several bases upstream and downstream of the dimer, and the segment of DNA between these two cuts is then enzymatically removed. DNA pol I replaces the missing nucleotides with the correct ones and DNA ligase seals the gap in the sugar-phosphate backbone.

Figure (PageIndex<6>): Bacteria have two mechanisms for repairing thymine dimers. (a) In nucleotide excision repair, an enzyme complex recognizes the distortion in the DNA complex around the thymine dimer and cuts and removes the damaged DNA strand. The correct nucleotides are replaced by DNA pol I and the nucleotide strand is sealed by DNA ligase. (b) In photoreactivation, the enzyme photolyase binds to the thymine dimer and, in the presence of visible light, breaks apart the dimer, restoring the base pairing of the thymines with complementary adenines on the opposite DNA strand.

The direct repair (also called light repair) of thymine dimers occurs through the process of photoreactivation in the presence of visible light. An enzyme called photolyase recognizes the distortion in the DNA helix caused by the thymine dimer and binds to the dimer. Then, in the presence of visible light, the photolyase enzyme changes conformation and breaks apart the thymine dimer, allowing the thymines to again correctly base pair with the adenines on the complementary strand. Photoreactivation appears to be present in all organisms, with the exception of placental mammals, including humans. Photoreactivation is particularly important for organisms chronically exposed to ultraviolet radiation, like plants, photosynthetic bacteria, algae, and corals, to prevent the accumulation of mutations caused by thymine dimer formation

  1. During mismatch repair, how does the enzyme recognize which is the new and which is the old strand?
  2. How does an intercalating agent introduce a mutation?
  3. What type of mutation does photolyase repair?

Identifying Bacterial Mutants

One common technique used to identify bacterial mutants is called replica plating. This technique is used to detect nutritional mutants, called auxotrophs, which have a mutation in a gene encoding an enzyme in the biosynthesis pathway of a specific nutrient, such as an amino acid. As a result, whereas wild-type cells retain the ability to grow normally on a medium lacking the specific nutrient, auxotrophs are unable to grow on such a medium. During replica plating (Figure (PageIndex<7>)), a population of bacterial cells is mutagenized and then plated as individual cells on a complex nutritionally complete plate and allowed to grow into colonies. Cells from these colonies are removed from this master plate, often using sterile velvet. This velvet, containing cells, is then pressed in the same orientation onto plates of various media. At least one plate should also be nutritionally complete to ensure that cells are being properly transferred between the plates. The other plates lack specific nutrients, allowing the researcher to discover various auxotrophic mutants unable to produce specific nutrients. Cells from the corresponding colony on the nutritionally complete plate can be used to recover the mutant for further study.

Figure (PageIndex<7>): Identification of auxotrophic mutants, like histidine auxotrophs, is done using replica plating. After mutagenesis, colonies that grow on nutritionally complete medium but not on medium lacking histidine are identified as histidine auxotrophs.

Why are cells plated on a nutritionally complete plate in addition to nutrient-deficient plates when looking for a mutant?

The Ames Test

The Ames test, developed by Bruce Ames (1928&ndash) in the 1970s, is a method that uses bacteria for rapid, inexpensive screening of the carcinogenic potential of new chemical compounds. The test measures the mutation rate associated with exposure to the compound, which, if elevated, may indicate that exposure to this compound is associated with greater cancer risk. The Ames test uses as the test organism a strain of Salmonella typhimurium that is a histidine auxotroph, unable to synthesize its own histidine because of a mutation in an essential gene required for its synthesis. After exposure to a potential mutagen, these bacteria are plated onto a medium lacking histidine, and the number of mutants regaining the ability to synthesize histidine is recorded and compared with the number of such mutants that arise in the absence of the potential mutagen (Figure (PageIndex<8>)). Chemicals that are more mutagenic will bring about more mutants with restored histidine synthesis in the Ames test. Because many chemicals are not directly mutagenic but are metabolized to mutagenic forms by liver enzymes, rat liver extract is commonly included at the start of this experiment to mimic liver metabolism. After the Ames test is conducted, compounds identified as mutagenic are further tested for their potential carcinogenic properties by using other models, including animal models like mice and rats.

Figure (PageIndex<8>): The Ames test is used to identify mutagenic, potentially carcinogenic chemicals. A Salmonella histidine auxotroph is used as the test strain, exposed to a potential mutagen/carcinogen. The number of reversion mutants capable of growing in the absence of supplied histidine is counted and compared with the number of natural reversion mutants that arise in the absence of the potential mutagen.


Changes in the MLH1, MSH2, MSH6, PMS2, or EPCAM gene have been found in people with Lynch syndrome.

The MLH1, MSH2, MSH6, and PMS2 genes are involved in repairing errors that occur when DNA is copied in preparation for cell division (a process called DNA replication ). Because these genes work together to fix DNA errors, they are known as mismatch repair (MMR) genes. Mutations in any of these genes prevent the proper repair of DNA replication errors. As the abnormal cells continue to divide, the accumulated errors can lead to uncontrolled cell growth and possibly cancer. Mutations in the MLH1 or MSH2 gene tend to lead to a higher risk (70 to 80 percent) of developing cancer in a person's lifetime, while mutations in the MSH6 or PMS2 gene have a lower risk (25 to 60 percent)of cancer development.

Mutations in the EPCAM gene also lead to impaired DNA repair, although the gene is not itself involved in this process. The EPCAM gene lies next to the MSH2 gene on chromosome 2 and certain EPCAM gene mutations cause the MSH2 gene to be turned off (inactivated). As a result, the MSH2 gene's role in DNA repair is impaired, which can lead to accumulated DNA errors and cancer development.

Although mutations in these genes predispose individuals to cancer, not all people with these mutations develop cancerous tumors.

Learn more about the genes associated with Lynch syndrome


Watch the video: CRISPR babies and CCR5-delta32 (May 2022).