Resume:
This work is an overview of the genome and proteome of the bacterium Bacteroides uniformis.
Keywords:
Bacteroides Uniformis ,gram-negative , genome , proteins
Introduction:
Goal:
The purpose of this work is to familiarize you with general information, as well as the genetic structure of Bacteroides uniformis, based on data on its genome.
Taxanomy:
- Domain: Bacteria
- Phylum: Bacteroidetes
- Class: Bacteroidia
- Order: Bacteroidales
- Family: Bacteroidaceae
- Genus: Bacteroides
- Species: Bacteroides Uniformis [1]
General information:
Bacteroides species are gram-negative, anaerobic, bile-resistant bacteria residing in the gut and constitute approximately 25% of the intestinal gut microbiota. These commensal bacteria can affect the intestinal immune system, interacting with the host, or by production of certain molecules that ultimately alter the intestinal immune response. Bacteroides uniformis has the ability to deconjugate bile acids, thus interfering with their metabolism. This leads, in particular, to impaired absorption of fats and fat-soluble compounds.[2]
Bacteroides uniformis thrive in fiber-enriched environments as they have complex enzymatic machinery to utilize oligo- and poly-saccharides as nutrients. [3]
Methods:
- The code for calculating the length of all nucleotides , proving the rule of Chargaff, length of GC nucleotides and their extent in sequence
- I used the COUNTIFS function to create a bar on which I later built a histogram ( Picture 1) Practical work 8
- The code for finding the number of appearances of stop codons
- In order to make descriptive statistics i used such commands as =MIN , =MAX ,=AVERAGE, =STDEV.P , =MEDIAN
Results:
The genome of bacteroides uniformis is represented by a single closed chromosome Using the python programming methods i found out that this chromosome contains 4728573 nucleotides . The number of each nucleotide is shown in a Chart 1
| A | T | C | G | N |
|---|---|---|---|---|
| 126 | 126 | 1097 | 110 | 100 |
As I noticed , the amount of complementary nucleotides (A ~ T , G~C )is quite similar. So this sequence follows the seconds rule of Chargaff [4] . What is more interesting is that the chromosome of my bacteria is not limited to A,G,C,T nucleotides . It has exactly 100 ‘N’ nucleotides which are believed to exist only to create diversity at V(D)J junctions during lymphocyte development. The addition of these nucleotides are aided by an enzyme called Terminal deoxynucleotidyl transferase (TdT) . Does it mean that bacteroides uniformis might somehow be connected with the lymphocyte development ? Not really . At least for now since the mechanism of how TdT works is unclear . I also calculated the extent of GC in a sequence which turned out to be 46.5% . This extent is impressively similar to that of Desulfotalea psychrophila LSv54 ( 46.5%)[5]
In a chart 2 we can see the number of appearances of stop codons . The most used stop codon is “TAA” . Thus, the correlation between GC-composition of the genome and frequencies of usage of stop codons is proved[6]
| Stop codon | Number | Frequency |
|---|---|---|
| TGA | 960 | 0.2583 |
| TAA | 2216 | 0.5963 |
| TAG | 540 | 0.1453 |
In a chart 3 we can the descriptive statistics : mean length, standard deviation , median , minimum / maximum length
| mean length | standart deviation | median | minimum length | maximum length |
|---|---|---|---|---|
| 380.98 | 249.99 | 330.5 | 26 | 1980 |
Using Excel I made a histogram(Diagram 1) of
protein length with a bin length equal to 51 .
Looking at this histogram , we may notice that
the most common length of proteins is around
100-200 nucleotides
References:
[1] Taxanomy
[2] https://www.sciencedirect.com/topics/medicine-and-dentistry/bacteroides-uniformis
[3] https://www.frontiersin.org/articles/10.3389
[4] Chargaff's rules