Replichoresandgeneorientation - PRABI-Doua: Homepage · 2012-08-27 · Bacterialgenomestructures...
18
Bacterial genome structures Replichores and gene orientation Replichores and gene orientation 1 Introduction 2 Chromosomes Topology & Counts 3 Genome size 4 Replichores and gene orientation 5 Chirochores 6 G+C content 7 Codon usage 77 [email protected] Bacterial genome structures
Transcript of Replichoresandgeneorientation - PRABI-Doua: Homepage · 2012-08-27 · Bacterialgenomestructures...
Bacterial genome structures
Replichores and gene orientation
Replichores and gene orientation
1 Introduction
2 Chromosomes Topology & Counts
3 Genome size
4 Replichores and gene orientation
5 Chirochores
6 G+C content
7 Codon usage
77 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Replichores: origin and terminus of replication
Eukaryota Bacteria
Many origins A single origin
78 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
There are two replichores per chromosome
79 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Archae & Bacteria
80 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Looking for the origin
81 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Looking for the origin in E. coli
82 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Looking for the origin in B. burgdorferi
83 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Zoom at the origin
84 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
How replication works?
http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.
cgi?it=swf::535::535::
/sites/dl/free/0072437316/120076/micro04.swf
85 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Leading and lagging CDS
86 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Are genes equally reparted on both strands?
Study this yourself:Download the bsubt_2011.zip file for B. subtilis on the classwebpage, and study the repartition of genes on the genome,relatively to the origin and terminus of replication and the strand.
You will need to know the position of the origin and terminus ofreplication. As a good approximation, use:
Origin : 0 bp
Terminus : 2.1 Mb
Bonus: How to define the two first colonnes of the .ptt file fromthe third one? In ? In another language?
87 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
More leading CDS than lagging CDS
88 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
For those about to rock. . .
89 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Another way to see it: CDS skew Lactobacillus
plantarum
CDS skew is proportionnal to thenumber of CDS on the ”+”strandminus the number of CDS on the ”-”strand, while going along thegenome.Can you do the same graph for B.subtilis?
90 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
CDS skew in B. subtilis
91 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Collisions between polymerases
92 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Connection with essentiality
Rocha, E.P.C. & Danchin, A. (2003) Nature Genetics, 34:377-378.
93 [email protected] Bacterial genome structures
Bacterial genome structures
Replichores and gene orientation
Essentiality and the quest for the smallest autonomous
genome
2 main approaches:
By deletion : define all essential genes by single deletion,coupled deletion, bioinformatics prediction, and try to deleteall the non-essential genes.
By addition : synthetize an entirely new genome doing onlywhat you want it to do : this is called synthetic biology.
The minimal genome should contain 250-300 genes(estimation from Koonin E., Nature Rev. Micobiol. (2003) 1)
94 [email protected] Bacterial genome structures
