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The Fundamental Similarity of All
Living Things
Microbial Ecology
138023
Oded Beja
All cells encode information on the form of DNA
• DNA in all cells is composed of
-the same four bases adenine, guanine, cytosine, thymine
-the same sugar (D-ribose)
-assembled in the same chemical structure and stereochemistry
All cells encode information on the form of DNA
• DNA in all cells is composed of
-the same four bases adenine, guanine, cytosine, thymine
-the same sugar (D-ribose)
-assembled in the same chemical structure and stereochemistry
•Information in DNA is stored using a Universal 3-letter code
All cells encode information on the form of DNA
• DNA in all cells is composed of
-the same four bases adenine, guanine, cytosine, thymine
-the same sugar (D-ribose)
-assembled in the same chemical structure and stereochemistry
•Information in DNA is stored using a Universal 3-letter code
•DNA synthesis is handled the same way in all organisms
All cells encode information on the form of DNA
• DNA in all cells is composed of
-the same four bases adenine, guanine, cytosine, thymine
-the same sugar (D-ribose)
-assembled in the same chemical structure and stereochemistry
•Information in DNA is stored using a Universal 3-letter code
•DNA synthesis is handled the same way in all organisms
•The function of DNA is carried out via transcription into RNA using
polymerases
RNA
RNA is used to direct protein synthesis based
on information in DNA
•RNA in all cells has the same structure
-same 4 bases (ACGU)and sugar,
-same structure and stereochemistry
•All cells have the same types of RNA:rRNA, tRNA,
These RNAs are very much alike in sequence and
structure in all cells
ex:The rRNA in all organisms are greater than 50% identical
in sequence and 80% in structure
Proteins direct most of the cell catalysis and
structure
•Proteins in all cells use the same 20 amino acids,
synthesized in the same way,and use the same
post-translation modification
Proteins direct most of the cell catalysis and
structure
•Proteins in all cells use the same 20 amino acids,
synthesized in the same way,and use the same
post-translation modification
•Protein synthesis is carried out via translation in the
same way in all organisms
Proteins direct most of the cell catalysis and
structure
•Proteins in all cells use the same 20 amino acids,
synthesized in the same way,and use the same
post-translation modification
•Protein synthesis is carried out via translation in the
same way in all organisms
•Most of the reactions catalyzed by these proteins are
the same and the enzymes that carry them out are
very-much alike in amino acid sequence and 3dimensional structure, and mechanism of action
All cells are bound by a lipoprotein membrane
•strictly control what goes in and come out of the cell (transport
systems)
•defines the cell, separating inside and outside
So,all cells are pretty-much alike
What does this means?
1-All organisms share a common ancestry
2-The last common ancestor of all living things was a
complex organism
3-The last common ancestor had all the biochemistry that
is now universal
The diversity of extant life (modern life) is in
peripheral biochemistry details!
Phylogenetics and the
Trees of Life
Microbial Ecology
138023
Oded Beja
Prokaryotic species:
A prokaryote whose 16S rRNA sequence differs by
more than 3% (or is less than 97% identical) from
that of all other organisms should be considered a
new species (3% of 1500 nucleotides = 45
nucleotides).
The DNA from 2 bacteria whose 16S rRNA
sequences are less than 97%identical usually
hybridize to less than 70%, a minimal value for
organisms to be considered being of the same
species.
Molecular Phylogenetics
is the study of evolutionary relationships among
organisms by using molecular data such as DNA
and protein sequences
A phylogenetic classification (cladistics) is based
upon evolutionary relationships i .e. upon common
ancestry, in contrast to a phenetic classification
(phenetics, numerical taxonomy) which is based
upon overall similarity
Nomenclature of trees
•Trees can be made with nucleotide or protein
Sequences
•Homologs are genes/proteins with a common
evolutionary ancestor reflected by sequence
Similarity
•Orthologs are homologs that diverged due to
Speciation
•Paralogs are homologs that diverged due to
duplication
Homology is...
the similarity that is the result of inheritance from a
common ancestor - identification and analysis of
homologies is central to phylogenetics
Two sequences are homologous if they share a
common evolutionary ancestry. THERE ARE NO
DEGREES OF HOMOLOGY
A phylogenetic tree represents the evolutionary / geneological
relationships between a collection of organisms (or molecular
sequences). It is composed of branches and nodes
Only one branch connects any two nodes.There are internal
branches (-----) and external branches (_). Branches define the
topology of the tree, that is the relationships among taxa in terms
of ancestry
Two alternative representation of a phylogenetic tree:
(a) Unscaled branches (phenogram): terminal nodes are lined up
and nodes are positioned proportionally to time of divergence
(b)Scaled branches (dendrogram): lengths of branches are
proportional to number of molecular changes along them (e.g.
nucleotide or aa substitution). The evolutionary distance between two
organisms is the total length of all the branches that connect them
Other methods for determining
phylogenetic relationships
1-DNA:DNA hybridization
2-DNA base composition
3-Serology
4-Lipid profiling
5-RFLP analysis
6-rRNA spacer sequence analysis
7-Ribotyping
8-Phenotypic markers
Lateral gene transfer
In prokaryotes
Standart model of the universal SSU rRNA tree
‫זיהוי‬
‫•‬
‫דרגת דמיון גבוהה בין התורם למקבל עבור התכונה הנבדקת‪.‬‬
‫• חלוקה פילוגנטית עבור התכונה בין המקבל לזנים הקרובים אליו‬
‫אבולציונית‪.‬‬
‫• מה בין ‪convergent evolution‬לבין ‪lateral gene transfer‬‬
‫• ניתוח גנטי‪-‬מולקולרי של רצפי ‪DNA‬‬
‫שיטות זיהוי‬
‫• ניתוח מידע ממאגרים לגבי הומולוגיות בין גנים‬
‫• חיפוש רצפים בעלי הרכב לא אופיני‬
‫•‪GC content‬‬
‫•‪codon usage‬‬
‫• שרידי רצפים הקשורים לאינטגרציה של ‪LGT‬‬
‫מנגנונים נפוצים למעבר של חומר גנטי בין חיידקים‬
Gene transfer agents (GTAs)
GTAs discovered in the purple nonsulfur bacterium
Rhodobacter capsulatus are host-encoded viruslike
elements that package random fragments of the host
chromosome and are found in the genome of almost
every sequenced member of the alpharoteobacteria
order Rhodobacterales
‫תפוצת ‪ DNA‬ממקור לטרלי בגנומים בקטריאלים‬
Standart model of the universal SSU rRNA tree