Difference between revisions of "RRNA operon 2009"

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Ribosomal RNA ([http://en.wikipedia.org/wiki/RRNA rRNA]) is the central component of the ribosome, the protein manufacturing machinery of all living cells. The function of the rRNA is to provide a mechanism for decoding mRNA into amino acids and to interact with the tRNAs during translation by providing peptidyl transferase activity.The tRNA then brings the necessary amino acids corresponding to the appropriate mRNA codon. Archaea contains either a single rDNA operon or multiple copies of the operon.  
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<p>Ribosomal RNA ([http://en.wikipedia.org/wiki/RRNA rRNA]) is the central component of the ribosome, the protein manufacturing machinery of all living cells. The function of the rRNA is to provide a mechanism for decoding mRNA into amino acids and to interact with the tRNAs during translation by providing peptidyl transferase activity.The tRNA then brings the necessary amino acids corresponding to the appropriate mRNA codon. Archaea contains either a single rDNA operon or multiple copies of the operon. </p>
  
Archea usually contains three kinds of rRNA: 16S, 5S and 23S. 5S and 23S are part of the large ribosomal subunit, whereas 16S is part of the small robosomal unit and is responsible for recognizing the Shine-Delgarno sequences on most mRNAs. 16S is one of the most highly conserved sequences in any genome. 23S has peptidyl transferase activity and assists in binding adjacent amino acids during translation of an mRNA. Chloramphenicol acts by binding to the 23S rRNA so studying this gene in particular might explain why our species is chloramphenicol resistant.
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<p>Archea usually contains three kinds of rRNA: 16S, 5S and 23S. 5S and 23S are part of the large ribosomal subunit, whereas 16S is part of the small robosomal unit and is responsible for recognizing the Shine-Delgarno sequences on most mRNAs. 16S is one of the most highly conserved sequences in any genome. 23S has peptidyl transferase activity and assists in binding adjacent amino acids during translation of an mRNA. Chloramphenicol acts by binding to the 23S rRNA so studying this gene in particular might explain why our species is chloramphenicol resistant. </p>
  
  
Strangely enough, All the suggested 5S rRNAs in our genome were identical, as shown in the BLAST2 comparison here:
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All the suggested 5S rRNA genes in our genome were identical, as shown in the BLAST2 comparison here:
 +
 
 
[[Image:Mr11.png]]
 
[[Image:Mr11.png]]
 +
 +
Typically in prokaryotes, rRNA genes are linked in transcription in the order of (5') 16s-23s-5s (3'). However, this only occurs at one instance in our genome.
  
 
== 5s rRNA (445..583(+); 1766895..1767033(-); 1962..2100(+)), all three consisted of 139 identical base pairs.==  
 
== 5s rRNA (445..583(+); 1766895..1767033(-); 1962..2100(+)), all three consisted of 139 identical base pairs.==  
 +
 +
The 5s rRNA is a component of the 50s ribosomal subunit in prokaryotes, and it often includes sites of inhibition for some antibiotics in some species.
 +
  
 
[[Image:5srRNAmr.png]]
 
[[Image:5srRNAmr.png]]
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==16s rRNA (1770405..1771883(-); 1479bp): Top three species with similar 16s rRNA sequences==
 
==16s rRNA (1770405..1771883(-); 1479bp): Top three species with similar 16s rRNA sequences==
  
[[Image:MR2.png]]
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'''[[Image:MR2.png]]'''
  
 
[[Image:MR3.png]]
 
[[Image:MR3.png]]
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== 23S rRNA 644033000; 23S; 1863 bp Top thee genes with significant similarity==
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== 23S rRNA ==
 +
 
 +
ID Number: 644033000
 +
 
 +
Location: (1..1863(+))
  
[[Image:23S31.png]]
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Length: 1863 bp
  
[[Image:23S32.png]]
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Top three genes with significant similarity according to BLAST:
  
[[Image:23S33.png]]
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[[Image:330001.png]]
  
 +
[[Image:330002.png]]
  
== 23S rRNA 644032999; 23S; 1908bp Top three genes with significant similarity:==
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[[Image:330003.png]]
  
[[Image:23S21.png]]
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== 23S rRNA ==
  
[[Image:23S22.png]]
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ID Number: 644032999
  
[[Image:23S23.png]]
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Location: (3109294..3111201(+))
  
The only significant genes were found in the Halomicrobium mukihataei genome. This is suspicious since it shares no commonalities with other closely related species.
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Length: 1908bp
  
== 23S rRNA 644031592; 2907bp: Top two genes with significant similarity:==
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Top three genes with significant similarity according to BLAST:  
  
 +
[[Image:329991.png]]
  
[[Image:23S12.png]]
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[[Image:329992.png]]
  
[[Image:23S13.png]]
+
[[Image:329993.png]]
  
== 23S rRNA 644029745; 23S; 349bp: Top three genes with significant similarity:==  
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== 23S rRNA ==
 +
 
 +
ID Number: 644031592
 +
 
 +
Location: 1767129..1770035 (-)
 +
 
 +
Length: 2907bp
 +
 
 +
Top three genes with significant similarity according to BLAST:
 +
 
 +
[[Image:315921.png]]
 +
 
 +
[[Image:315922.png]]
 +
 
 +
[[Image:315923.png]]
 +
 
 +
== 23S rRNA ==
 +
 
 +
ID Number: 644029745
 +
 
 +
Length: 349bp
 +
 
 +
Top three genes with significant similarity according to BLAST:
  
 
[[Image:23short1.png]]
 
[[Image:23short1.png]]
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This gene was, by far, the shortest 23S rRNA. 23s rRNA is usually a large molecule so this struck us as odd.
 
This gene was, by far, the shortest 23S rRNA. 23s rRNA is usually a large molecule so this struck us as odd.
 +
 +
==Missing rRNAs==
 +
 +
We also wondered why our genome did not seem to contain 18S or 28S rRNA. 28S and 18S are normally found in eukaryotic genomes and we would not expect to find it in the species we are studying.

Latest revision as of 14:35, 3 September 2009

Ribosomal RNA (rRNA) is the central component of the ribosome, the protein manufacturing machinery of all living cells. The function of the rRNA is to provide a mechanism for decoding mRNA into amino acids and to interact with the tRNAs during translation by providing peptidyl transferase activity.The tRNA then brings the necessary amino acids corresponding to the appropriate mRNA codon. Archaea contains either a single rDNA operon or multiple copies of the operon.

Archea usually contains three kinds of rRNA: 16S, 5S and 23S. 5S and 23S are part of the large ribosomal subunit, whereas 16S is part of the small robosomal unit and is responsible for recognizing the Shine-Delgarno sequences on most mRNAs. 16S is one of the most highly conserved sequences in any genome. 23S has peptidyl transferase activity and assists in binding adjacent amino acids during translation of an mRNA. Chloramphenicol acts by binding to the 23S rRNA so studying this gene in particular might explain why our species is chloramphenicol resistant.


All the suggested 5S rRNA genes in our genome were identical, as shown in the BLAST2 comparison here:

Mr11.png

Typically in prokaryotes, rRNA genes are linked in transcription in the order of (5') 16s-23s-5s (3'). However, this only occurs at one instance in our genome.

5s rRNA (445..583(+); 1766895..1767033(-); 1962..2100(+)), all three consisted of 139 identical base pairs.

The 5s rRNA is a component of the 50s ribosomal subunit in prokaryotes, and it often includes sites of inhibition for some antibiotics in some species.


5srRNAmr.png

16s rRNA (1770405..1771883(-); 1479bp): Top three species with similar 16s rRNA sequences

MR2.png

MR3.png

MR4.png

16s rRNA (3107428..3108907(+); 1480bp): Top three species with similar 16s rRNA sequences

Mr5.png

Mr6.png

Mr7.png


16s rRNA (218960..219414(+); 455bp): Top three species with similar 16s rRNA sequences

Mr8.png

Mr9.png

Mr10.png


23S rRNA

ID Number: 644033000

Location: (1..1863(+))

Length: 1863 bp

Top three genes with significant similarity according to BLAST:

330001.png

330002.png

330003.png

23S rRNA

ID Number: 644032999

Location: (3109294..3111201(+))

Length: 1908bp

Top three genes with significant similarity according to BLAST:

329991.png

329992.png

329993.png

23S rRNA

ID Number: 644031592

Location: 1767129..1770035 (-)

Length: 2907bp

Top three genes with significant similarity according to BLAST:

315921.png

315922.png

315923.png

23S rRNA

ID Number: 644029745

Length: 349bp

Top three genes with significant similarity according to BLAST:

23short1.png

23Short2.png

23Short3.png

This gene was, by far, the shortest 23S rRNA. 23s rRNA is usually a large molecule so this struck us as odd.

Missing rRNAs

We also wondered why our genome did not seem to contain 18S or 28S rRNA. 28S and 18S are normally found in eukaryotic genomes and we would not expect to find it in the species we are studying.