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 RNA polymerases

RNA is used to direct protein synthesis basedon 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 andstructure in all cells

ex:The rRNA in all organisms are greater than 50% identicalin sequence and 80% in structure

Proteins direct most of the cell catalysis andstructure

•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 andstructure

•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 thesame way in all organisms

Proteins direct most of the cell catalysis andstructure

•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 thesame way in all organisms

•Most of the reactions catalyzed by these proteins arethe same and the enzymes that carry them out arevery-much alike in amino acid sequence and 3-dimensional structure, and mechanism of action

All cells are bound by a lipoprotein membrane

•strictly control what goes in and come out of the cell (transportsystems)

•defines the cell, separating inside and outside

So,all cells are pretty-much alikeWhat 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 inperipheral biochemistry details!

Phylogenetics and theTrees of Life

Microbial Ecology

138023

Oded Beja

Prokaryotic species:

A prokaryote whose 16S rRNA sequence differs bymore than 3% (or is less than 97% identical) fromthat of all other organisms should be considered anew species (3% of 1500 nucleotides = 45nucleotides).

The DNA from 2 bacteria whose 16S rRNAsequences are less than 97%identical usuallyhybridize to less than 70%, a minimal value fororganisms to be considered being of the samespecies.

Molecular Phylogenetics is the study of evolutionary relationships amongorganisms by using molecular data such as DNAand protein sequences

A phylogenetic classification (cladistics) is basedupon evolutionary relationships i .e. upon commonancestry, in contrast to a phenetic classification(phenetics, numerical taxonomy) which is basedupon overall similarity

Nomenclature of trees

•Trees can be made with nucleotide or proteinSequences

•Homologs are genes/proteins with a commonevolutionary ancestor reflected by sequenceSimilarity

•Orthologs are homologs that diverged due toSpeciation

•Paralogs are homologs that diverged due toduplication

Homology is...

the similarity that is the result of inheritance from acommon ancestor - identification and analysis of

homologies is central to phylogenetics

Two sequences are homologous if they share acommon 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 upand nodes are positioned proportionally to time of divergence

(b)Scaled branches (dendrogram): lengths of branches areproportional 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

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

Other methods for determining phylogenetic relationships

Lateral gene transfer

In prokaryotes

Standart model of the universal SSU rRNA tree

דרגת דמיון גבוהה בין התורם למקבל עבור התכונה •הנבדקת.

חלוקה פילוגנטית עבור התכונה בין המקבל לזנים •הקרובים אליו אבולציונית.

lateral gene transferלבין convergent evolution מה בין •

DNAניתוח גנטי-מולקולרי של רצפי •

זיהוי

שיטות זיהוי

לגבי הומולוגיות בין גניםניתוח מידע ממאגרים •

בעלי הרכב לא אופיני חיפוש רצפים •

• GC content

• codon usage

LGT שרידי רצפים הקשורים לאינטגרציה של •

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

ממקור לטרלי בגנומים בקטריאלים DNA תפוצת

Standart model of the universal SSU rRNA tree