Genetic Version

In a strange genetic version of the Russian doll, scientists have discovered the genome of a bacterial parasite nestled inside the genome of its host. The findings, published today in the journal Science, suggest that organisms might quickly acquire new genes and functions through the large-scale transfer of genes. The parasite, known as Wolbachia, invades the eggs and sperm of many different types of insects, ensuring that it is passed down to the host's offspring. In this case, scientists discovered the bacterium's genome within the chromosome of its fruit-fly host. While microbiologists have previously seen cases of gene swapping between microbes or between parasites and their hosts, this is the first example of such an extensive exchange. According to a press release from the University of Rochester, "This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago," says W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, who is not connected to the study. "This is stunning evidence for increased frequency of gene transfer." "It didn't seem possible at first," says [Jack] Werren, professor of biology at the University of Rochester and a world-leading authority on the parasite, called Wolbachia. "This parasite has implanted itself inside the cells of 70 percent of the world's invertebrates, coevolving with them. And now, we've found at least one species where the parasite's entire or nearly entire genome has been absorbed and integrated into the host's. The host's genes actually hold the coding information for a completely separate species." A similar phenomenon may have happened in our own distant past. "In our very own cells and those of nearly all plants and animals are mitochondria, special structures responsible for generating most of our cells' supply of chemical energy. These were once bacteria that lived inside cells, much like Wolbachia does today. Mitochondria still retain their own, albeit tiny, DNA, and most of the genes moved into the nucleus in the very distant past. Like Wolbachia, they have passively exchanged DNA with their host cells. It's possible Wolbachia may follow in the path of mitochondria, eventually becoming a necessary and useful part of a cell. In a way, Wolbachia could be the next mitochondria," says Werren. "A hundred million years from now, everyone may have a Wolbachia organelle."

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Gene expression

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as rRNA genes or tRNA genes, the product is a functional RNA. Several steps in the gene expression process may be modulated, including the transcription step and translation step and the post-translational modification of a protein. Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation, morphogenesis and the versatility and adaptability of any organism. Gene regulation may also serve as a substrate for evolutionary change, since control of the timing, location, and amount of gene expression can have a profound effect on the functions (actions) of the gene in the organism. Transcription The gene itself is typically a long stretch of DNA and does not perform an active role. It is a blueprint for the production of RNA. The production of RNA copies of the DNA is termed transcription, and is performed by RNA polymerase, which adds one RNA nucleotide at a time to a growing RNA strand. This RNA is complementary to the DNA nucleotide being read, i.e. a T on the DNA means an A is added to the RNA. However, In RNA the nitrogen base Uracil is inserted instead of Thymine. Wherever there is an Adenine on the DNA strand, a Uracil is inserted into the complementary RNA strand. I.e the mRNA complement of a DNA strand reading "TAC" would be transcribed as "AUG", which is translated into the amino acid methionine, which is generally the starting point in a messenger RNA for expressing a protein. RNA processing Transcription creates a primary transcript of RNA at the place where the gene was located. This transcript often needs to be altered by enzymes. RNA processing, also known as post-transcriptional modification, can start already during transcription, as is the case for e.g. splicing where the spliceosome removes introns from newly formed parts of the RNA.[ Introns are RNA segments which are not found in the mature RNA, although they can function as precursors for e.g. snoRNA which are a group of RNAs that direct nucleotide modification of other RNAs. In some cases large aggregates of RNA and RNA processing factors are formed, notably the nucleolus where ribosomal RNA localises to be processed by snoRNAs and their partner enzymes. These chop the primary ribosomal RNA transcripts into the correct segments and alter some of its nucleotides into e.g. pseudouridine. RNA export While some RNAs function in the nucleus, many other RNAs in eukaryotes need to be transported through the nuclear pores and into the cytosol, including all the RNA types involved in protein synthesis.[ In some cases the RNA is additionally transported to a specific part of the cytoplasm, such as a synapse, they are then towed by motor proteins that bind through linker proteins to specific sequences (called "zipcodes") on the RNA. Translation For most RNA, the mature RNA is the gene product (see non-coding RNA). In the case of messenger RNA however, the RNA is but an information carrier for the synthesis of a protein. Each triplet of nucleotides of the coding region of a messenger RNA corresponds to a bindning site for a transfer RNA. Transfer RNAs carry amino acids, and these are chained together by the ribosome. The ribosome helps transfer RNA bind to messenger RNA and takes the amino acid from each tranfer RNA and makes a structure-less protein out of it. Some proteins have parts that should be within a membrane, these parts are moved into the membrane by the signal recognition particle which binds to the ribosome when it finds a signal sequence on the nascent amino acid chain. Folding Enzymes called chaperones assist the newly formed protein to attain (fold into) the 3-dimensional structure it needs to function. Similarly, RNA chaperones help RNAs attain their functional shapes. Protein export Many proteins that are destined for other parts of the cell than the cytosol. A commonly used mechanism for transporting these proteins to where they should be is translocation to the endoplasmatic reticulum, followed by transport via the Golgi apparatus.

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Vomitoxin

Vomitoxin, also known as deoxynivalenol (DON), is a type B trichothecene, an epoxy-sesquiterpeneoid. This mycotoxin occurs predominantly in grains such as wheat, barley, oats, rye, and maize, and less often in rice, sorghum, and triticale. The occurrence of deoxynivalenol is associated primarily with Fusarium graminearum (Gibberella zeae) and F. culmorum, both of which are important plant pathogens which cause Fusarium head blight in wheat and Gibberella ear rot in maize. A direct relationship between the incidence of Fusarium head blight and contamination of wheat with deoxynivalenol has been established. The incidence of Fusarium head blight is strongly associated with moisture at the time of flowering (anthesis), and the timing of rainfall, rather than the amount, is the most critical factor. Furthermore, deoxynivalenol contents are significantly affected by the susceptibility of cultivars towards Fusarium species, previous crop, tillage practices, and fungicide use F. graminearum grows optimally at a temperature of 25 °C and at a water activity above 0.88. F. culmorum grows optimally at 21 °C and at a water activity above 0.87. The geographical distribution of the two species appears to be related to temperature, F. graminearum being the commoner species and occurring in warmer climates. Deoxynivalenol has been implicated in incidents of mycotoxicoses in both humans and farm animals. When compared to other trichothecene mycotoxins which can form in grains and forages, vomitoxin is relatively mild. Reduced feed intake, and the accompanying decrease in performance, are the only symptoms of vomitoxin toxicity livestock producers will likely encounter. This response to vomitoxin appears to occur through the central nervous system. Vomitoxin belongs to a class of mycotoxins (tricothecenes) which are strong protein inhibitors. Inhibition of protein synthesis following exposure to vomitoxin causes the brain to increase its uptake of the amino acid tryptophan and, in turn, its synthesis of serotonin. Increased levels of serotonin are believed to be responsible for the anorexic effects of DON and other tricothecenes. Irritation of the gastrointestinal tract may also play a role in reducing feed intake... This fact may also partially explain the high incidence of pars esaughageal stomach ulcers observed in sows off feed during feed refusal. • Human foods: Vomitoxin is not a known carcinogen as with aflatoxin. Large amounts of grain with vomitoxin would have to be consumed to pose a health risk to humans. The FDA has established a level of 1 ppm (parts per million) restriction of vomitoxin. • Companion animals: Dogs and cats are restricted to 5 ppm and of grains and grain byproducts and that the grains not exceed 40% percent of the diet. • Livestock and farm animals: In animals and livestock, vomitoxin causes a refusal to feed and lack of weight gain when fed above advised levels. Restrictions are set at 10 ppm for poultry and ruminating beef and feedlot cattle older than 4 months. Ingredients may not exceed 50% of the animal's diet. Dairy cow limits are set at 2 ppm.

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A Genome within a Genome

In a strange genetic version of the Russian doll, scientists have discovered the genome of a bacterial parasite nestled inside the genome of its host. The findings, published today in the journal Science, suggest that organisms might quickly acquire new genes and functions through the large-scale transfer of genes. The parasite, known as Wolbachia, invades the eggs and sperm of many different types of insects, ensuring that it is passed down to the host's offspring. In this case, scientists discovered the bacterium's genome within the chromosome of its fruit-fly host. While microbiologists have previously seen cases of gene swapping between microbes or between parasites and their hosts, this is the first example of such an extensive exchange. According to a press release from the University of Rochester, "This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago," says W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, who is not connected to the study. "This is stunning evidence for increased frequency of gene transfer." "It didn't seem possible at first," says [Jack] Werren, professor of biology at the University of Rochester and a world-leading authority on the parasite, called Wolbachia. "This parasite has implanted itself inside the cells of 70 percent of the world's invertebrates, coevolving with them. And now, we've found at least one species where the parasite's entire or nearly entire genome has been absorbed and integrated into the host's. The host's genes actually hold the coding information for a completely separate species." A similar phenomenon may have happened in our own distant past. "In our very own cells and those of nearly all plants and animals are mitochondria, special structures responsible for generating most of our cells' supply of chemical energy. These were once bacteria that lived inside cells, much like Wolbachia does today. Mitochondria still retain their own, albeit tiny, DNA, and most of the genes moved into the nucleus in the very distant past. Like Wolbachia, they have passively exchanged DNA with their host cells. It's possible Wolbachia may follow in the path of mitochondria, eventually becoming a necessary and useful part of a cell. In a way, Wolbachia could be the next mitochondria," says Werren. "A hundred million years from now, everyone may have a Wolbachia organelle."

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DNA Transcription

DNA transcription is a process that involves the transcribing of genetic information from DNA to RNA. DNA is housed within the nucleus of our cells. It controls cellular activity by coding for the production of enzymes and proteins. The information in DNA is not directly converted into proteins, but must first be copied into RNA. This ensures that the information contained in the DNA does not become tainted. DNA consists of four nucleotide bases [adenine (A), guanine (G), cytosine (C) and thymine (T)] that are paired together (A-T and C-G) to give DNA its double helical shape. DNA is transcribed by an enzyme called RNA polymerase. Specific nucleotide sequences tell RNA polymerase where to begin and where to end. RNA polymerase attaches to the DNA at a specific area called the promoter region. The DNA strand opens and allows RNA polymerase to transcribe only a single strand of DNA into a single stranded RNA polymer called messenger RNA (mRNA). Like DNA, RNA is composed of nucleotide bases. RNA however, contains the nucleotides adenine, guanine, cytosine and uricil (U). When RNA polymerase transcribes the DNA, guanine pairs with cytosine and adenine pairs with uricil. RNA polymerase moves along the DNA until it reaches a terminator sequence. At that point, RNA polymerase releases the mRNA polymer and detaches from the DNA. Since proteins are constructed in the cytoplasm of the cell by a process called translation, mRNA must cross the nuclear membrane to reach the cytoplasm. Once in the cytoplasm, mRNA along with ribosomes and another RNA molecule called transfer RNA, work together to produce proteins. Proteins can be manufactured in large quantities because a single DNA sequence can be transcribed by many RNA polymerase molecules at once.

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Steps of DNA Replication

1)The first major step for the DNA Replication to take place is the breaking of hydrogen bonds between bases of the two antiparallel strands. The unwounding of the two strands is the starting point. The splitting happens in places of the chains which are rich in A-T. That is because there are only two bonds between Adenine and Thymine (there are three hydrogen bonds between Cytosine and Guanine). Helicase is the enzyme that splits the two strands. The initiation point where the splitting starts is called "origin of replication".The structure that is created is known as "Replication Fork".

2) One of the most important steps of DNA Replication is the binding of RNA Primase in the the initiation point of the 3'-5' parent chain. RNA Primase can attract RNA nucleotides which bind to the DNA nucleotides of the 3'-5' strand due to the hydrogen bonds between the bases. RNA nucleotides are the primers (starters) for the binding of DNA nucleotides. 3) The elongation process is different for the 5'-3' and 3'-5' template. a)5'-3' Template: The 3'-5' proceeding daughter strand -that uses a 5'-3' template- is called leading strand because DNA Polymerase ä can "read" the template and continuously adds nucleotides (complementary to the nucleotides of the template, for example Adenine opposite to Thymine etc). b)3'-5'Template: The 3'-5' template cannot be "read" by DNA Polymerase ä. The replication of this template is complicated and the new strand is called lagging strand. In the lagging strand the RNA Primase adds more RNA Primers. DNA polymerase å reads the template and lengthens the bursts. The gap between two RNA primers is called "Okazaki Fragments". The RNA Primers are necessary for DNA Polymerase å to bind Nucleotides to the 3' end of them. The daughter strand is elongated with the binding of more DNA nucleotides. 4) In the lagging strand the DNA Pol I -exonuclease- reads the fragments and removes the RNA Primers. The gaps are closed with the action of DNA Polymerase (adds complementary nucleotides to the gaps) and DNA Ligase (adds phosphate in the remaining gaps of the phosphate - sugar backbone). Each new double helix is consisted of one old and one new chain. This is what we call semiconservative replication. 5) The last step of DNA Replication is the Termination. This process happens when the DNA Polymerase reaches to an end of the strands. We can easily understand that in the last section of the lagging strand, when the RNA primer is removed, it is not possible for the DNA Polymerase to seal the gap (because there is no primer). So, the end of the parental strand where the last primer binds isn't replicated. These ends of linear (chromosomal) DNA consists of noncoding DNA that contains repeat sequences and are called telomeres. As a result, a part of the telomere is removed in every cycle of DNA Replication. 6) The DNA Replication is not completed before a mechanism of repair fixes possible errors caused during the replication. Enzymes like nucleases remove the wrong nucleotides and the DNA Polymerase fills the gaps. Similar processes also happen during the steps of DNA Replication of prokaryotes though there are some differences.

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RNA - Transcription

Introduction:

The differences in the composition of RNA and DNA have already been noted. In addition, RNA is not usually found as a double helix but as a single strand. However, the single polynucleotide strand may fold back on itself to form portions which have a double helix structure like the tertiary structure of proteins.

The biosynthesis of RNA, called transcription, proceeds in much the same fashion as the replication of DNA and also follows the base pairing principle. Again, a section of DNA double helix is uncoiled and only one of the DNA strands serves as a template for RNA polymerase enzyme to guide the synthesis of RNA. After the synthesis is complete, the RNA separates from the DNA and the DNA recoils into its helix.

The transcription of a single RNA strand is illustrated in the graphic on the left. One major difference is that the heterocyclic amine, adenine, on DNA codes for the incorporation of uracil in RNA rather than thymine as in DNA. Remember that thymine is not found in RNA and do not confuse the replacement of uracil in RNA for thymine in DNA in the transcription process. For example, thymine in DNA still codes for adenine on RNA not uracil, while the adenine on DNA codes for uracil in RNA.

Note that the new RNA (red) is identical to non coding DNA with the exception of uracil where thymine was located in DNA.

There are three major types of RNA which will be fully explained in a later section. Although RNA is synthesized in the nucleus, it migrates out of the nucleus into the cytoplasm where it is used in the synthesis of proteins.

RNA Transcription Process:

The RNA transcription process occurs in three stages: initiation, chain elongation, and termination.

The first stage occurs when the RNA Polymerase-Promoter Complex binds to the promoter gene in the DNA. This also allows for the finding of the start sequence for the RNA polymerase. The promoter enzyme will not work unless the sigma protein is present (shown in blue in graphic). Specific sequences on the non coding strand of DNA are recognized as the signal to start the unwinding process.

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Transcription

Transcription is the synthesis of RNA under the direction of DNA. RNA synthesis, or transcription, is the process of transcribing DNA nucleotide sequence information into RNA sequence information. Both nucleic acid sequences use complementary language, and the information is simply transcribed, or copied, from one molecule to the other. DNA sequence is enzymatically copied by RNA polymerase to produce a complementary nucleotide RNA strand, called messenger RNA (mRNA), because it carries a genetic message from the DNA to the protein-synthesizing machinery of the cell. One significant difference between RNA and DNA sequence is the presence of U, or uracil in RNA instead of the T, or thymine of DNA. In the case of protein-encoding DNA, transcription is the first step that usually leads to the expression of the genes, by the production of the mRNA intermediate, which is a faithful transcript of the gene's protein-building instruction. The stretch of DNA that is transcribed into an RNA molecule is called a transcription unit. A DNA transcription unit that is translated into protein contains sequences that direct and regulate protein synthesis in addition to coding the sequence that is translated into protein. The regulatory sequence that is before (upstream (-), towards the 5' DNA end) the coding sequence is called 5' untranslated region (5'UTR), and sequence found following (downstream (+), towards the 3' DNA end) the coding sequence is called 3' untranslated region (3'UTR). Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for copying DNA; therefore, transcription has a lower copying fidelity than DNA replication. As in DNA replication, RNA is synthesized in the 5' → 3' direction (from the point of view of the growing RNA transcript). Only one of the two DNA strands is transcribed. This strand is called the template strand, because it provides the template for ordering the sequence of nucleotides in an RNA transcript. The other strand is called the coding strand, because its sequence is the same as the newly created RNA transcript (except for uracil being substituted for thymine). The DNA template strand is read 3' → 5' by RNA polymerase and the new RNA strand is synthesized in the 5'→ 3' direction. A polymerase binds to the 3' end of a gene (promoter) on the DNA template strand and travels toward the 5' end.

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