The goal of this blog is to concentrate new information on Ribozymes for reference to those interested in our topic. In addition to our blog, we are participating in a computing grid sponsored by RNAworld
whose aim is to use bioinformatic data to predict possible RNA molecules, as well as analyze unknown enzymatic activity.
Hi all, The questions concerning your paper are below. My advice is for you to try to divide them up roughly evenly among your group members. You are even welcome to post the answers independently if you'd like; just be sure to reiterate the questions. Please come see me if you need help! 1. Why, from an evolutionary standpoint, might it be informative for scientists or doctors to study naturally-occurring ribozymes in non-human organisms when investigating human ribozyme function? 2. Use the NCBI website to perform a protein BLAST on the Accession number CAB54141.1 (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome0). Paste the accession number into the box, and then hit the BLAST button. Name five different taxa that come up in your results. What does that tell you about this ribozyme-associated protein? 3. Refer to the first paragraph under “Hammerhead ribozyme” on page 223. The authors assert that, during the course of RNA evolution, this motif arose multiple times. What is the evolutionary term for the process in which phenotypes arise independently in multiple lineages? Do you believe that binding motifs are phenotypes? So then, do you think that this term can be applied to the evolution of RNA lineages? 4. The last paragraph (page 227) references “in vitro selection”. Describe this methodology and how it could be used to shed light on the diversity of ribozymes comprising the RNA world. Bonus: Do you buy the RNA World hypothesis? Briefly, why or why not? -Dr. Walker
2. Five different taxa from the pBlast were Triturus carnifex Italian Crested Newt ;Heterocephalus glaber Naked mole rat; Mus musculus mouse; Ailuropoda melanoleuca Giant Panda;Cavia porcellus Guinea Pig. This shows that this ribozyme-associated protein has several analogs in a wide range of species. This suggests a kind of convergent evolution has taken place.
3. The evolutionary term for the process in which phenotypes arises independently in multiple lineages is known as convergent evolution. I believe that since the differences in binding motifs allowed the Hammerhead ribozyme to be efficient at self-splicing and replication than other ribozymes, it can be considered a type of phenotype that influences how efficiently it can work; thus being favored by natural selection. Since this ribozyme arose many times beforehand in different methods, one should be able to use the term convergent evolution to describe the evolution of RNA lineages.
1. Why, from an evolutionary standpoint, might it be informative for scientists or doctors to study naturally-occurring ribozymes in non-human organisms when investigating human ribozyme function?
The RNA World hypothesis attempts to explain the evolution of genetic information carriers in a pre-DNA world. Therefore, we are speculating a time before there existed prokaryotic and eukaryotic structures. When we examine the naturally occurring ribozymes and analogous RNA structures, we essentially examine these hypothetical remnants of the RNA World. There is the potential that, not very distantly in the past, our ancestors were still depending on the sole catalytic activity of RNAs, before a transition to the currently understood co-factors and proteins which assist in replication and protein synthesis. Tetrahymena, for example, was the first organism documented as having RNA molecules form catalytic active sites and included a self-splicing pre-ribosomal RNA. Tetrahymena has served as a model organism in Biology for many years because it has two different types of cell nuclei and allows for unique experimentation in gene expression. We essentially use this organism to identify what sorts of sequences we want to look for in other organisms, including humans. Other uses, which include projects in the RNA World grid, include screening for certain non-coding RNAs that are believed necessary to the ability of many pathogens to infect their host. Such pathogens include Mycobacterium tuberculosis and Mycobacterium leprae, which cause tuberculosis and leprosy, respectively.
4. The last paragraph (page 227) references “in vitro selection”. Describe this methodology and how it could be used to shed light on the diversity of ribozymes comprising the RNA world.
“In vitro”, literally meaning “in glass” in Latin, refers to that which is outside the living body or in an artificial environment. Within the context of this paper, in vitro selection is the process whereby functional ribozymes are screened for certain catalytic activities within a controlled environment. They first generated a pool of random RNA sequence and selected sequences for specific catalytic activity, a process known as activity selection. These selected sequences are then synthesized into DNA using reverse transcription and the DNA sequences are then amplified using polymerase chain reactions that multiply the number of copies of the sequences. This paper specifically refers to the discoveries made using this process and include “identification of ribozymes that form a nucleotide from a base plus a sugar, synthesize amide bonds, form Michael adducts such as those involved in the methylation of uridine monophosphate to give thymidine monophosphate, and form acyl-coenzyme A, which is found in many protein enzymes.” The importance of the in vitro selection technique is very significant to the RNA World hypothesis because it lends credibility to the idea that these ribozymes, or enzymatically active RNA molecules, can have a diverse range of biological activity that would potentially allow for the necessary functions required by genetic information carriers in the hypothetical time of transition from RNA as the main genetic information carrier to our current Central Dogma of Biology. If a ribozyme can catalyze an important reaction, and its analogs persists in a diversity of organisms, then it may be hypothesized that some very distant ancestor could have existed and utilized these primitive mechanisms. A very important note to make on this method of in vitro selection is that, since these RNA sequences are screened for activity outside a living cell in an artificial environment, we can assert that these activities are possible without the assistance of the other “machinery” of a cell such as the normal proteins that assist in the process of the selected biological activities.
Bonus: Do you buy the RNA World hypothesis? Briefly, why or why not?
We all accept the idea. The hypothesis seems to be the most reasonable in terms of what we already know about the significance of RNA in the Central Dogma of Biology. Proof of ribozyme’s potential for enzymatic activity lends credibility to the idea that ribozymes may have been capable of synthesizing simple genetic sequences. This proof includes the fact that ribozymes can in fact catalyze some chemical reactions in the absence of co-factors that are necessary in the current understanding of the biological system. Although, with a hypothesis such as the RNA World, it is difficult to prove beyond a reasonable doubt that this was in fact how the evolution of genetic information carriers took place. But, as more support for the hypothesis is generated, we should consider the hypothesis as a distinct possibility.
Hi all,
ReplyDeleteThe questions concerning your paper are below. My advice is for you to try to divide them up roughly evenly among your group members. You are even welcome to post the answers independently if you'd like; just be sure to reiterate the questions. Please come see me if you need help!
1. Why, from an evolutionary standpoint, might it be informative for scientists or doctors to study naturally-occurring ribozymes in non-human organisms when investigating human ribozyme function?
2. Use the NCBI website to perform a protein BLAST on the Accession number CAB54141.1 (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome0). Paste the accession number into the box, and then hit the BLAST button. Name five different taxa that come up in your results. What does that tell you about this ribozyme-associated protein?
3. Refer to the first paragraph under “Hammerhead ribozyme” on page 223. The authors assert that, during the course of RNA evolution, this motif arose multiple times. What is the evolutionary term for the process in which phenotypes arise independently in multiple lineages? Do you believe that binding motifs are phenotypes? So then, do you think that this term can be applied to the evolution of RNA lineages?
4. The last paragraph (page 227) references “in vitro selection”. Describe this methodology and how it could be used to shed light on the diversity of ribozymes comprising the RNA world.
Bonus: Do you buy the RNA World hypothesis? Briefly, why or why not?
-Dr. Walker
2. Five different taxa from the pBlast were Triturus carnifex Italian Crested Newt ;Heterocephalus glaber Naked mole rat; Mus musculus mouse; Ailuropoda melanoleuca Giant Panda;Cavia porcellus Guinea Pig. This shows that this ribozyme-associated protein has several analogs in a wide range of species. This suggests a kind of convergent evolution has taken place.
Delete3. The evolutionary term for the process in which phenotypes arises independently in multiple lineages is known as convergent evolution. I believe that since the differences in binding motifs allowed the Hammerhead ribozyme to be efficient at self-splicing and replication than other ribozymes, it can be considered a type of phenotype that influences how efficiently it can work; thus being favored by natural selection. Since this ribozyme arose many times beforehand in different methods, one should be able to use the term convergent evolution to describe the evolution of RNA lineages.
1. Why, from an evolutionary standpoint, might it be informative for scientists or doctors to study naturally-occurring ribozymes in non-human organisms when investigating human ribozyme function?
ReplyDeleteThe RNA World hypothesis attempts to explain the evolution of genetic information carriers in a pre-DNA world. Therefore, we are speculating a time before there existed prokaryotic and eukaryotic structures. When we examine the naturally occurring ribozymes and analogous RNA structures, we essentially examine these hypothetical remnants of the RNA World. There is the potential that, not very distantly in the past, our ancestors were still depending on the sole catalytic activity of RNAs, before a transition to the currently understood co-factors and proteins which assist in replication and protein synthesis. Tetrahymena, for example, was the first organism documented as having RNA molecules form catalytic active sites and included a self-splicing pre-ribosomal RNA. Tetrahymena has served as a model organism in Biology for many years because it has two different types of cell nuclei and allows for unique experimentation in gene expression. We essentially use this organism to identify what sorts of sequences we want to look for in other organisms, including humans. Other uses, which include projects in the RNA World grid, include screening for certain non-coding RNAs that are believed necessary to the ability of many pathogens to infect their host. Such pathogens include Mycobacterium tuberculosis and Mycobacterium leprae, which cause tuberculosis and leprosy, respectively.
4. The last paragraph (page 227) references “in vitro selection”. Describe this methodology and how it could be used to shed light on the diversity of ribozymes comprising the RNA world.
“In vitro”, literally meaning “in glass” in Latin, refers to that which is outside the living body or in an artificial environment. Within the context of this paper, in vitro selection is the process whereby functional ribozymes are screened for certain catalytic activities within a controlled environment. They first generated a pool of random RNA sequence and selected sequences for specific catalytic activity, a process known as activity selection. These selected sequences are then synthesized into DNA using reverse transcription and the DNA sequences are then amplified using polymerase chain reactions that multiply the number of copies of the sequences. This paper specifically refers to the discoveries made using this process and include “identification of ribozymes that form a nucleotide from a base plus a sugar, synthesize amide bonds, form Michael adducts such as those involved in the methylation of uridine monophosphate to give thymidine monophosphate, and form acyl-coenzyme A, which is found in many protein enzymes.” The importance of the in vitro selection technique is very significant to the RNA World hypothesis because it lends credibility to the idea that these ribozymes, or enzymatically active RNA molecules, can have a diverse range of biological activity that would potentially allow for the necessary functions required by genetic information carriers in the hypothetical time of transition from RNA as the main genetic information carrier to our current Central Dogma of Biology. If a ribozyme can catalyze an important reaction, and its analogs persists in a diversity of organisms, then it may be hypothesized that some very distant ancestor could have existed and utilized these primitive mechanisms. A very important note to make on this method of in vitro selection is that, since these RNA sequences are screened for activity outside a living cell in an artificial environment, we can assert that these activities are possible without the assistance of the other “machinery” of a cell such as the normal proteins that assist in the process of the selected biological activities.
Bonus: Do you buy the RNA World hypothesis? Briefly, why or why not?
ReplyDeleteWe all accept the idea. The hypothesis seems to be the most reasonable in terms of what we already know about the significance of RNA in the Central Dogma of Biology. Proof of ribozyme’s potential for enzymatic activity lends credibility to the idea that ribozymes may have been capable of synthesizing simple genetic sequences. This proof includes the fact that ribozymes can in fact catalyze some chemical reactions in the absence of co-factors that are necessary in the current understanding of the biological system. Although, with a hypothesis such as the RNA World, it is difficult to prove beyond a reasonable doubt that this was in fact how the evolution of genetic information carriers took place. But, as more support for the hypothesis is generated, we should consider the hypothesis as a distinct possibility.