EVE161 Lecture 3

Lecture 3:

EVE 161: 
Microbial Phylogenomics
!

Lecture #3:
Era I: Woese and the Tree of Life
!
UC Davis, Winter 2014
Instructor: Jonathan Eisen

Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014

Where we are going and where we have been

• Previous lecture:
! 2. Evolution of DNA sequencing
• Current Lecture:
! 3. Woese and the Tree of Life
• Next Lecture:
! 4. Modern view of Tree of Life


Era I: rRNA Tree of Life

Era I:
rRNA Tree of Life


!3

• Tree of life vs. Trees of Life


!4

Phylogeny was central to Darwin’s Work on Natural Selection


!5

Phylogeny
• Phylogeny is a description of the evolutionary history of
relationships among organisms (or their parts).
• This is portrayed in a diagram called a phylogenetic
tree.
• Phylogenetic trees are used to depict the evolutionary
history of populations, species and genes.
• The Tree of Life refers to the concept that all living
organisms are related to one another through shared
ancestry.

Ch. 25.1

!6

Darwin and a Single Tree of Life

George Richmond. Darwin Heirlooms
Trust

Darwin Origin of Species 1859

!

Set stage for “tree thinking”


!7

How many trees of tree
The default class life?

If this tree included all
major groups of organisms
a

b

c

d

e

h

g

f

What does this
imply about the #
of times life
evolved?

!8

Common ancestry of all life

a

b

c

d

e

h

g

f

MRCA

!9


a

b

c

This implies a single
origin of life,
sometime before
MRCA

d

e

h

g

f

MRCA


!10


a

b

c

This implies a single
origin of life,
sometime before
MRCA

d

e

h

MRCA

g

f

And thus that
there is one
“Tree of Life”


!11

What if life originated twice?

But no theoretical reason why we could living
organisms could not have multiple separate
ancestries
a

b

c

d

e

h

g

f

Origin 1
Origin 2


!12

How many trees of life?

• How do we distinguish two hypotheses?
! 1. a single origin (and thus a single tree of life)
2. multiple origins (and thus multiple separate
trees)?
!

• What data might support one hypothesis versus
the other?


!13

Universal homologies

• Characters that are found in the same state an all
organisms are considered
“universal” (remember “presence” can be a
state)
• Characters (i.e., features like the smiley face)
that are inherited from a common ancestor are
homologous
• Homologous characters that are found in the
same state in all organisms are “universal
homologies”


!14

12.3 From Gene to Protein


!15

12.6 The Genetic Code


!16

The Ribosome


!17

Universal homologies: examples
• Molecular and cellular features
! Use of DNA as a genetic material
! Use of ACTG in DNA
! Use of ACUG in RNA
! Three letter genetic code
! Central dogma (DNA -> RNA -> protein)
! Lipoprotein cell envelope
! 20 core amino acids in proteins
• Specific complexes and genes
! Ribosomal proteins and RNA
! RNA polymerase proteins


!18

Universal homologies: examples

• Data matrix for universal homologies
!

DNA

Three letter
code

DNA-> RNA> protein

E. coli

+

+

+

Yeast

+

+

+

Humans

+

+

+

M. jannascii

+

+

+

Organism

• What does this mean in terms of the number of
“origins” of life?

!19

How to infer a phylogenetic tree


!20


a

b

c

d

e

h

g


f

!21


a

b

c

d

e

h

g


f

!22


a

b

c

d

e

h

g


f

!23


a

b

c

d

e

h

g


f

!24


a

b

c

d

e

h

g


f

!25

a

b

c

d

e

h

g


f

!26

a

b

c

d

e

h

g


f

!27

a

b

c

d

e

h

g


f

!28

a

b

c

d

e

h

g


f

!29

a

b

c

d

e

h

g

f

Problem: homologous trait needs to have a
single origin

!30

a

b

c

d

e

h

g

f

Must connect the trees

!31

a

b

c

d

e

h

g

f

Must connect the trees

!32

a

b

c

d

e

h

g

Conclusion: existence of universal
homologies Davis EVE161 Course Taught by Jonathan Eisen Winter 2014
implies a single tree of life
Slides for UC

f

!33

a

b

c

d

e

h

g

f

MRCA

!34

Universal homologies

• What does the existence of “universal
homologies” mean?
• The key to the implications of “universal
homologies” to the Tree of Life, is that
homologous traits should be derived from a
single, common ancestral trait.
• This implies a single origin of life.
• Note - lateral transfer can lead to organisms
sharing homologous features EVEN if the
organisms have a separate origin


!35

LUCA


!36

How to Build a Tree of Life?


!37

• Data matrix for universal homologies
!

DNA

Three letter
code

DNA-> RNA> protein

E. coli

+

+

+

Yeast

+

+

+

Humans

+

+

+

M. jannascii

+

+

+

Organism

• What does this mean in terms of the relationships
among different branches?

!38

• For building a single tree including all organisms
• Need traits that are homologous between all organisms
but which have variable states
• Examples???
! Until 1960s these were hard to come by
! Researchers focused instead on relationships within
particular branches of the Tree of Life
! Within sub-branches, more possible traits to use (e.g.,
bones in mammals)


!39

Ernst Haeckel 1866

Plantae
Protista
Animalia

!40

Whittaker – Five Kingdoms 1969

Monera
Protista
Plantae
Fungi
Animalia

!41

Carl Woese

http://mcb.illinois.edu/faculty/
proﬁle/1204


!42

Two papers for today
Proc. Natl. Acad. Sci. USA
Vol. 74, No. 10, pp. 4537-4541, October 1977

Evolution

Classification of methanogenic bacteria by 16S ribosomal RNA
characterization
(comparative oligonucleotide cataloging/phylogeny/molecular evolution)

GEORGE E. Fox* t, LINDA J. MAGRUM*, WILLIAM E. BALCHt, RALPH S. WOLFEf,
AND CARL R. WOESE**
Departments of *Genetics and Development and tMicrobiology, University of Illinois, Urbana, Illinois 61801

Communicated by H. A. Barker, August 10, 1977

residues represented by hexamers and larger in catalog A and
in catalog B and their overlap of common sequences, respectively. The association coefficient, SAB, SO defined provides
what is generally an underestimate of the true degree of
homology between two catalogs because related but nonidentical oligomers are not considered. The matrix of SAB values for
each binary comparison among the members of a given set of
organisms is used to generate a dendrogram by average linkage
(between the merged groups) clustering. The resulting denmetabolic capacity to growstructure oxidizing hydroanaerobically by of the prokaryotic strictly speaking, phyletic because no "ancestral
drogram is, domain: The primary
Phylogenetic
catalog" has been postulated. However, it is clear from the
gen and reducing carbon dioxide to methane (1-3). Their rekingdoms
molecular nature of the data that the topology of this dendrolationships to one another and to other microbes remain virunknown. Protein and nucleic acid primary structures
gram would closely resemble, if not be identical to, that of a
tually(archaebacteria/eubacteria/urkaryote/16S ribosomal RNA/molecular phylogeny)
are perhaps the most reliable indicators of phylogenetic relaphylogenetic tree based upon such ancestral catalogs.
tionships R. WOESE AND GEORGE E.as the 16S ribosomal
CARL (4-6). By using a molecule, such Fox* constrained
RNA, that is readily isolated, ubiquitous, and highly
RESULTS
inDepartment of Geneticspossible to relateUniversity ofmost distant of
sequence (7), it is and Development, even the Illinois, Urbana, Illinois 61801
The 10 organisms whose 16S ribosomal RNA oligonucleotide
microbial species. To date, approximately 60 bacterial species
Communicated by T. M. Sonneborn, August16S ribosomal RNA
18,1977
catalogs are listed in Tables 1 and 2 cover all of the major types
have been characterized in terms of their
of methanogens now in pure culture except for 2; we have been
primary structures (refs. 6-9, unpublished data). We present
A phylogenetic analysis based upon by this
to construct a culture of Methanococcus between domains:
ABSTRACT
here results of a comparative study of the methanogensribosomal unable to obtain phylogenetic classificationsvanniehfi (19), and
RNA sequence characterization reveals one another and to
that living systems Methanobacterium mobile (20) comparabledifficult to grow
Prokaryotic kingdoms are not has proven to eukaryotic ones.
method, which shows their relationships to
represent one
of
This should sequences in by, an bear little terminology. The
typical bacteria. of three aboriginal lines (ii) descent: (i) the eu- and label. The be recognizedTable 1appropriateresemblance to
bacteria, comprising all typical bacteria; the archaebacteria, those for typical bacteria (refs. the prokaryotic domain we think
6-9; unpublished data). Fig. 1
highest
containing methanogenic bacteria; and (iii) the urkaryotes, now is ashould phylogenetic unit inthe SAB values in Table 3."primary
dendrogram derived from
called an "urkingdom"-or perhaps It
METHODScomponent EVE161 Courseseen be by Jonathan Eisen Winter 2014 can
Slides for UC
Taught methanogens comprise two major divisions. The
represented in the cytoplasmic Davis of eukaryotic be kingdom." This would recognize the qualitative distinction
that-the
cells.
ABSTRACT
The 16S ribosomal RNAs from 10 species of
methanogenic bacteria have been characterized in terms of the
oligonucleotides produced by T1 RNase digestion. Comparative
analysis of these data reveals the methanogens to constitute a
distinct -phylogenetic group containing two major divisions.
These Natl. Acad. Sci. USAto be only distantly related to typical
Proc. organisms appear
bacteria.No. 11, pp. 5088-5090, November 1977
Vol. 74,
Evolution
The methane-producing bacteria are a poorly studied collection
of morphologically diverse organisms that share the common

!43

Vol. 74, No. 10, pp. 4537-4541, October 1977

Evolution

Classification of methanogenic bacteria by 16S ribosomal RNA
characterization
(comparative oligonucleotide cataloging/phylogeny/molecular evolution)

GEORGE E. Fox* t, LINDA J. MAGRUM*, WILLIAM E. BALCHt, RALPH S. WOLFEf,
AND CARL R. WOESE**
Departments of *Genetics and Development and tMicrobiology, University of Illinois, Urbana, Illinois 61801

Communicated by H. A. Barker, August 10, 1977

ABSTRACT
The 16S ribosomal RNAs from 10 species of
methanogenic bacteria have been characterized in terms of the
oligonucleotides produced by T1 RNase digestion. Comparative
analysis of these data reveals the methanogens to constitute a
distinct -phylogenetic group containing two major divisions.
These organisms appear to be only distantly related to typical
bacteria.

residues represented by hexamers and larger in catalog A and
in catalog B and their overlap of common sequences, respectively. The association coefficient, SAB, SO defined provides
what is generally an underestimate of the true degree of
homology between two catalogs because related but nonidentical oligomers are not considered. The matrix of SAB values for
each binary comparison among the members of a given set of
organisms is used to generate a dendrogram by average linkage
(between the merged groups) clustering. The resulting dendrogram is, strictly speaking, phyletic because no "ancestral
catalog" has been postulated. However, it is clear from the
molecular nature of the data that the topology of this dendrogram would closely resemble, if not be identical to, that of a
phylogenetic tree based upon such ancestral catalogs.

The methane-producing bacteria are a poorly studied collection
of morphologically diverse organisms that share the common
metabolic capacity to grow anaerobically by oxidizing hydrogen and reducing carbon dioxide to methane (1-3). Their relationships to one another and to other microbes remain virtually unknown. Protein and nucleic acid primary structures
are perhaps the most reliable indicators of phylogenetic relaSlides for UC Davis the 16S Course Taught by Jonathan Eisen Winter 2014
tionships (4-6). By using a molecule, such asEVE161 ribosomal

!44

• ABSTRACT:

!
• The 16S ribosomal RNAs from 10 species of
methanogenic bacteria have been characterized in terms
of the oligonucleotides produced by T(1) RNase
digestion. Comparative analysis of these data reveals the
methanogens to constitute a distinct phylogenetic group
containing two major divisions. These organisms appear
to be only distantly related to typical bacteria.


!45

4538

Proc. Nati.'Acad. Sci. USA 74 (1977)

Evolution: Fox et al.

Oligonucleotide

sequence
5-mers
CCCCG

Table 1. Oligonucleotide catalogs for 16S rRNA of 10 methanogens
Present in
Present in
OligonuOligonucleotide
cleotide
organism
organism
number
number
sequence
sequence
1-lO;l,5,8

CCCAG
CCACG
ACCCG
CCAAG
CACAG
CAACG
ACACG
ACCAG
AACCG
ACAAG
AAACG
AAAAG

6
10
10
9
9

CUCCG
CCCUG
UCCAG
CUCAG
OCAUG
UCACG
UACCG

4,7

ACCUG
ACUCG
AUCCG
UAACG
CAAUG
ACUAG
ACAUG
AUACG
AAUCG
UAAAG
AUAAG
AAAUG

UUCCG
CUUCG
UCCUG
CCUUG
CUCUG
UCUAG
UUCAG
CUAUG
UACUG
UAUCG
ACUUG
AUCUG
AUUCG
UUAAG
UAAUG
AUAUG
AAUUG
AUUAG
UUUCG
UUCUG
UCUUG
CUUUG
UUUAG
UUAUG
UUUUG
6-mers
CCCCAG

1-10;8-9

7-9
7

1-10;10
1-6;1,5

7-9

1,6,9-10

9

6-8s1
1-10
1-10

1-2,4-5
1-6,8
4-5;5
6
9
4-9

1-6;4
2-3,8-9

10
7
10
2

3-10;3,6-9;7

4

1-6,8;4
5-6,8
1-6;4
1

6,8
7

5,7-9;9
5

7-10;8-10
7-8

1-6,10
3-5,7-8
2-3,10
1-10;1-2,4,6,8,10
1-2,5,10;2
3-4,9
1-10;1-2,4-6,9

CCCUUG
CCUCUG
UCCCUG
CCUUAG
CUCUAG
CUUCAG
UCCUAG
UUCCAG
CCUAUG
CUACUG
UCACUG
CUAUCG
UCAUCG
CAUCUG
ACUCUG
ACCUUG
AUCCUG
UCUAAG
UUACAG
UAUCAG
UAUACG
UAAUCG
AUACUG
ACAUUG
AACUUG
AAUCUG
UAAAUG
AUUAAG
AAUAUG

4
1

4-5,7-9
1-6,10;1
7,9-10

.7-9

1-6,8-10

9
1-10
10

1-6,10
10;10

1-10;8--9
1-3,7
1-2,4-6
6,10

7-9
1-10

4,7-8

1-3
9
1-2
1-6
3

1-3,6
3,7-9

7-10

4,60

7-9
6-10
8-10

CCCUCG
CCUCAG
CUCCAG
UCCCAG
CCACUG
ACCUCG
CCUAAG
CUCAAG

5,8,10
5

AACCCCG
CCAACAG
CAACACG
CAAACCG
CCCUACG
CCCACUG

SUCCACCG
CCACCUG
2,7-10
CCCUAAG
4-5,9
9
UCACACG
CUACACG
1-3,5,10

4-6

UAACCCG

7
6
3
6
10
7-9
10
1

1-2,4,7-8

1-2,5

5UAUUUUG

UUCUUUG

4-6
3

1-4,6

UUUUUUG

1-3

2,8-10

8-mers
CCACAACG
ACCCCAAG
AAACCCCG

9

7

6,10

1-2,4-6,10

3-4

-1-4,7-8,10

1-2,4-6

UUUUUG

ACCACG
ACACCG
AAACCG

7-10
7
8
9
7

10
7-8
10
1
1
10

1
3
5-9
4
1-8
9

2,9

CCCCAG

1,3-6

1,3-6

UUCUUCG
UCUCUUG
CUUUAUG
UUUAUCG
UAUUUCG
AUUAUUG

3,7-8,10

1-5;1
1,4

~~~~~ACCCACG
ACCACCG

10
7-9

9
7
2
8
10
10
4
3

CUUUUG
UCUUUG

7-mers

AAAUCUG

8-1o

CUCCUUG
UCCCUUG
UUCUCCG
CUCUUAG
UACUUCG
UACUCUG
UCAUAUG
UAAUCUG
AAUUUAG

1-3,5,10
2,7
4,9;9

4,7,9

CCCUUAG
CAUCCUG
UACUCCG
AUCUCCG
ACCUUCG
UCCUAAG
UUACCAG
CUAACUG
UAACUCG
AUUCCAG
AUCAUCG
AAUCUCG
AACCUUG
UCUAAAG
CUUAAAG
CAAUAUG
AUACUAG
AAUCUAG

number

1-10
8
1-6
1-10
7

10
10

7
7-8
4-6
1-10
7-8
8
9
7
1-10

3
8-9

1-10;1l-7,9;7

AUACCCG
AACCUCG
CCUAAAG
UAACACG
AUAACCG
AAUCCAG
AACAUCG
AAAUCCG
UAAAAAG

organism

UAAAAUG

7,9

CCUUUG
CUUUCG
UCUCUG
UUCCUG
UCUUAG
CUAUUG
UUACUG
UAUUCG
AUUCUG
ACUUUG
UAUAUG

4,6

CACCAG

CCAUAG
CAUACG
ACACUG
AACCUG
AAUCCG
CUAAAG
UAAACG
ACUAAG
ACAAUG
AUAACG
AAUACG
AACAUG
AAACUG
AAAUCG
AAUAAG

Present in

10

10
3
2
8

1-9
7
7

UCCACCAG
CCCACAUG
CUCAACCG
ACCCUCAG
ACCACCUG
UAACACCG
AUCCCAAG
AAAUCCCG

1-2,5-6

CCCUCAUG
UACUCCCG

1-10
10

CCUAUCAG
CCUAACUG
CUUAACCG

7-8

8-9

4-6
10

7-8
3

4,7-10
5-6

AU(CCUC)CG
TUAAUCCCG

CUACAAUG
UACUACAG
UAAUACCG
AUUACCAG
AUAACCUG

1-3,5-10

1-3,5-6,9-10
1,5

9
7-8
8
7

1,3-6,8,10
1-6,10

2-3
1

1,3-4

4
5
10
5

4,7,9
9

1-10
10
7-9
3

6-8,10

Table 1 continues on following page.

!46

Proc. Nati. Acad. Sci. USA 74 (1977)


4539

Table 1. (continued)

Oligonu-

Present in

Oligonu-

Present in

Oligonu-

Present in

sequence

number

sequence

number

sequence

number

cleotide

organism

cleotide

organism

ACAAUCUG
AAAUCCUG
AUAAACUG
AUAAAUAG

9

1-2,6-9

AAUUAUCCG
UUUAAAACG
UAAACUAUG
AUAAUACUG

(CU,CCUU)CG

4
4

CUAUUACUG
UUAAAUUCG
UUUAAUAAG

9
1
2

UUAUAUUCG
UAUUUCUAG
UUUAUUAAG

2
9

CUUUUAUUG

6

AUCCUUCG
UCUAACUG
CUUAACUG
UAAUCCUG
UCUAAAUG
UUAAAUCG
CAUAUAUG
AAAUCUUG
AAAUUCUG
AUAAAUUG

3-6
2

1
2-3,5-6
1-3,6

1
10
10
10
2-3
1

7-9
7
7
2

1

cleotide

organism

UUUUUUUCCUG
UUUUUUUUAAG

1
2

12-mers
CCACCCAAAAAG
UCAAACCACCCG
UCAAACCAUCCG
ACAUCUCACCAG
CCACUCUUAACG
CCAUUCUUAACG
CUCAACUAUUAG
CCACUAUUAUUG
CAAUUAUUCCUG
CCACUUUUAUUG
CCAUUUUUAUUG

UUUUUAUUG
2,4
(CUA,CUUUUA)UUG
UUUUUUUCG
1
CUUUUCAG
613mr
2
UUCUCAUG
10-mers
UAAACUACACCUG
UUUAAUCG
9
7
AAUAACCCCG
(CAA,CCA)CAUUCUG
UAUCAUUG
9
2-3
UUUAAAUG
ACCACCUAUG
9UCAAAC
8
AAUCUCACCG
AUAAUUUUUCCUG
UUUAAUUG
1-8,10
AAAUCUCACG
4(UUU,CUU,CU)AAAUG
8
UAACUCAAAG
UUUUUUCG
2-3
AAACUUAAAG
1-10
14-mers
UUUUAUUG
1
10
ACCUUACCUG
AAAACUUUACAAUG
9-mers
UUACCAUCAG
3
AUUUUU(CCU,CU)UUG
4-5
CCCACCAAG
10
UACCUACUAG
1-10
CACACACCG
15mr
AAUCACUUCG
UCUAACACCCGs
8
(CCA,CAA)CAG
6
AACCCUUAUG
CAUAAACCCACCUUG
CCCAACAAG
7-9
9
UAAAUAACUG
AUAACCUAACCUUAG
AACCCCAAG
6
AAACCCAAG
4
6
UUCUUCACCG
AAUAAUACCCUAUAG
ACUCUACUUG
9AAUAAUACUCCAUAG
1
CCUCACCAG
8
CUUAACUAUG
AUAAUCUACCCUUAG
CCUACCAAG
6
AUACUAUUAG
2,4-5
CCUACAACG
10
AUAACCCCG
6,8,10
UUCCCUAUUG
AAAUCCUAUAAUCCCG
1-6
AAACCUCCG
UCUUCUUAAG
4
AAUCUCCUAUAAUCAUG
CACACUAAG
1-6
CAAUCUCUUAAACCUAG
AUAAACCCG
6
1
AUUUUUUUCG
UAAUCUCCUAAACCUG
UACUCCCAG
UUUUUGAAAUCCUAUAAUCCUG
UAAUCCCCG
7
AAUCCCCUG
1,3-6
11-mers
17-mers
CUUACCAAG
1-3
ACAACUCACCG
10
CAAUCUUUUAAACCUAG
3
(UC)ACACAUG
AAAUCCCACAG
6
UAAU(CCU,CU)AAACUUAG
2-3
(UC)ACAAUCG
CAUCUCACCAG
4
UCAUAACCG
AUAAU(CCU,CU)AAACCUG
7,9
UAACUCACCCG
CUAAUACCG
9
3
AAAUCUCACCG
ACCCUUAAG
18-mer
7
7,9
AAACACCUUCG
6
AACAAUCUCCUAAACCUG
AUAAUCCCG
9
AAAUCCCAUAG
AUAACCCUG
1-5
5
AUAAUACCG
24-mer
4-5
UCCCUCCCCUG
10
AUAUACAAG
9
(AAACA,UAAUCUCA)CAUAUCCUCCG
10
CCCAUCCUUAG
AAAUCCUAUAG
3
UCUUACCAG
10
UCACUAUCG
6
termini
5' end
UUUCAACAUAG
UAAUCCCUG
10
7,9
6
pAG
UAAUCCUCG
A(UA,UCA,CUA)UG
8
pAAUCCG
AAUUUCCCG
10
UUUCAAUAUAG
pAAUCUG
10
AAUCCUCUG
2
pAUUCUG
UCAUAAUCG
1,5
CUUUUCUUAAG
CUAAUACUG
1
1,3
CUUUUCAUUAG
CAUCAUAUG
2
10
3'end
UUCUUUAAUCG
7
AUAAUUCCG
10
AUCACCUCCUOH

1-2,4,6

8-10
7
1-6
4-6
1-3
10
7
2
8
5
3
10
6

~~~~~~~~~~~~~~~~~~~~~~~~~~UAAUACUCCAUAG9
3
5

9
~~~~~~~~~~~~~~~~~~~~~~~~~~~AAAACUUUACCAUG
7-8,10
2

1-

14
8
7
5

U4AUCCCAAACAGs

1-3,5-6UUUUU

4
4
7
4
5
3
1-2
9
8

10

4,6
5

1,
2,7-10
1-10

First column is oligonucleotide sequence; second column shows organisms in which that sequence is found. Organisms are designated by number
(see Fig. 1) as follows: 1, M. arbophilicum; 2, M. ruminantium strain PS; 3, M. ruminantium strain M-1; 4, M. formicicum; 5, M. sp. strain M~o.H.;
6, M. thermoautotrophicum; 7, Cariaco isolate JR-i; 8, Black Sea isolate JR-i; 9, Methanospirillum hungatii; 10, Methanosarcina barkeri.
Multiple occurrences of a sequence in a given Course Taught by Jonathan Eisen Winter 2014
Slidesa doubleUC Davis EVE161organism are denoted by repeating the organism's number in column 2: e.g., 1-4,6-8;3,7,;3 signifies
for occurrence in organism 7 and a triple occurrence in organism 3.

!47

4540


Proc. Nat

Table 2. Post-transcriptionally modified sequences and likely
counterparts
Occurrence in methanogens Occurrence in
IA
Sequence
IB
IIA
IIB typical bacteria
1.AACCUG
+
+
30%
AAUCUG
+
+
None
AAG
55%
2. UAACAAG
+
+
None
UAACAAG
+
+
None
UAACAAG
>95%
3. AUNCAACG +
+
None
ACNCAACG +
+
None
AX6CTAACG - >90%
4. NCCG
+
+
None
+
+
C((CC)G
None
N'CCG
>95%
5. CC(CCG
+
>95%
Post-transciptionally modified sequences in methanogens and their
likely counterparts in the bacteria that have been examined. In group
1, A is N-6-diMe (21), identified by electrophoretic mobilities of A
and AA and by total resistance to U2 nuclease. In group 2, U is partially resistant to pancreatic nuclease, the first A when modified is
still U2 nuclease sensitive; the second A is N-6-diMe. N in group 3 is
resistant to pancreatic nuclease but is electrophoretically U-like. X
stands for U or A. In group 4, N and N' are not cleaved by endonucle~aes; NC and N'C are electrophoretically distinguishable; C is
cleaved by pancreatic nuclease and has C-like electrophoretic prop,erties. In group 5, IC (21, 22) is not cleaved by pancreatic nuclease and
is readily deaminated by NH40H.

phylogenetic distinction

A
of this

apparent magnitude is

nication). The extent t

unique remains to be d
(iii) All other bacteri
single exception of the
glycan (26, 27). Howeve
examples) do not contai
personal communication
(iv) Table 2 shows th
16S ribosomal RNA in
ferent from that in typic
as well (D. Stahl, p
methanogens are the fi
terized (prokaryote or
called "common sequen
contain a

I"ICG

seque

U'ICG (the dot above a
cation; U
T) (L.
data).
It should be noted th
be completely unrelated
requirement of a strict
become the more impre
ogens have been charact
biochemistry and molec
It would appear that me
classified as a systemat
(inclusive of the blue-g
Although it cannot
methanogens represent
!48

ilarly, coenzyme F420, which handles low-potential electrons,
is present in all methanogens but so far is not found elsewhere

Note Added in Proof: Preliminary characterization of Methanobacterium mobile, a motile, Gram-negative, short rod, places this organism
in group IIA. Methanobacterium sp. strain AZ (30) has been shown
to be a strain of M. arbophilicum; SAB = 0.87 for the pair.
The work reported herein was performed under National Aeronautics and Space Administration Grant NSG-7044 and National

(25).
(ii) We have been unable to detect cytochromes in these organisms, and R. Thauer obtained no evidence for the presence
of quinones in M. thermoautotrophicum (personal commu-

Table 3. SAB values for each indicated binary comparison

Organism
1. M. arbophilicum

1

2

3

4

5

6

Organism
7

8

9

2. M. ruminantium PS
.66
3. M. ruminantium M-1
.60
.60
4. M. formicicum
.50
.48
.49
5. M. sp. M.o.H.
.53
.49
.51
.60
6. M. thermoautotrophicum
.52
.49
.51
.54
.60
7. Cariaco isolate JR-1
.25
.27
.25
.26
.23
.25
8. Black Sea isolate JR-1
.26
.28
.26
.27
.28
.29
.59
9. Methanospirillum hungatii
.20
.24
.21
.22
.23
.23
.51
.52
10. Methanosarcina barkeri
.24
.41
.29
.26
.24
.26
.34
.25
.33
11. Enteric-vibrio sp.
.08
.08
.11
.05
.06
.07
.09
.09
.10
12. Bacillus sp.
.10
.14
.11
.11
.12
.10
.08
.10
.10
13. Blue-green sp.
.10
.11
.10
.08
.09
.10
.10
.10
.08
The values given for enteric-vibrio sp., Bacillus sp., and blue-green sp. represent averages obtained from 11

species, respectively.

10

11

12

13

.10
.27
.08
.11
.24
.26
(9), 7 (6), and 4 (23) individual


!49

50

!50


Vol. 74, No. 11, pp. 5088-5090, November 1977
Evolution

Phylogenetic structure of the prokaryotic domain: The primary
kingdoms
(archaebacteria/eubacteria/urkaryote/16S ribosomal RNA/molecular phylogeny)

CARL R. WOESE AND GEORGE E. Fox*
Department of Genetics and Development, University of Illinois, Urbana, Illinois 61801

Communicated by T. M. Sonneborn, August 18,1977

to construct phylogenetic classifications between domains
Prokaryotic kingdoms are not comparable to eukaryotic ones
This should be recognized by, an appropriate terminology. Th
highest phylogenetic unit in the prokaryotic domain we thin
should be called an urkingdom-or perhaps primar
kingdom. This would recognize the qualitative distincti
between prokaryotic and eukaryotic kingdoms and emphasiz
The biologist has customarily structured his world in terms of
that the former have primary evolutionary status.
certain basic dichotomies. Classically, what was not plant was
The passage from one domain to a higher one then become
animal. The discovery that bacteria, which initially had been
a central problem. Initially one would like to know whether th
considered plants, resembled both plants and animals less than
is a frequent or a rare (unique) evolutionary event. It is trad
plants and animals resembled one another led to a reformulationally assumed-without evidence-that the eukaryot
tion of the issue in terms of a yet more basic dichotomy, that of
domain has arisen but once; all extant eukaryotes stem from
eukaryote versus prokaryote. The striking differences betweenTaught common ancestor, itself eukaryotic (2). A similar prejudice1
Slides for UC Davis EVE161 Course
by Jonathan Eisen Winter 2014
!5 hol

A phylogenetic analysis based upon ribosomal
ABSTRACT
RNA sequence characterization reveals that living systems
represent one of three aboriginal lines of descent: (i) the eubacteria, comprising all typical bacteria; (ii) the archaebacteria,
containing methanogenic bacteria; and (iii) the urkaryotes, now
represented in the cytoplasmic component of eukaryotic
cells.

Woese and Fox  

• Abstract: A phylogenetic analysis based upon ribosomal
RNA sequence characterization reveals that living
systems represent one of three aboriginal lines of
descent: (i) the eubacteria, comprising all typical bacteria;
(ii) the archaebacteria, containing methanogenic bacteria;
and (iii) the urkaryotes, now represented in the
cytoplasmic component of eukaryotic cells.


!52

12.3 From Gene to Protein


!53

The Ribosome


54
!54

rRNA structure


!55

rRNA Systematics

• All cellular organisms have ribosomes
• All have homologous subunits of the ribosomes including specific
ribosomal proteins and ribosomal RNAs (i.e., these are universally
homologous genes)
• Woese determined the sequences of ribosomal RNAs from different
species
• The sequences are highly similar but have some variation
• Each position in a rRNA can be considered a distinct character trait
• Each position has multiple possible character states (A, C, U, G)


!56

Why rRNA for Woese?

•
•
•
•

Universal

Highly conserved functionally

Evolves slowly

Easy to extract and sequence


!57

Woese Methods

•
•
•
•
•
•

Digest rRNA with T1 Rnase

2D electrophoresis

Fingerprint

Sequence each fragment

Oligonucleotide catalog

Association constant SAB = 2NAB/(NA+NB)

– NA = total number of nucleotides in catalog for A

– NB = total number in nucleotides in catalog for B

– NAB = total number in the shared catalog


Eubacteria

“A comparative analysis of these data,
summarized in Table 1, shows that the
organisms clearly cluster into several primary
kingdoms. The ﬁrst of these contains all of the
typical bacteria so far characterized .... (lots of
names here) ... It is appropriate to call this
urkingdom the eubacteria.”

61

Urkaryotes

• “A second group is deﬁned by the 18S
rRNAs of the eukaryotic cytoplasm-animal,
plant, fungal, and slime mold (unpublished
data).”

• (They call this lineage the urkaryotes)


Archaebacteria
“Eubacteria and urkaryotes correspond approximately to the conventional
categories prokaryote and eukaryote when they are used in a
phylogenetic sense. However, they do not constitute a dichotomy; they do
not collectively exhaust the class of living systems. There exists a third
kingdom which, to date, is represented solely by the methanogenic bacteria,
a relatively unknown class of anaerobes that possess a unique metabolism
based on the reduction of carbon dioxide to methane (19-21). These
bacteria appear to be no more related to typical bacteria than they are to
eukaryotic cytoplasms. Although the two divisions of this kingdom appear
as remote from one another as blue-green algae are from other eubacteria,
they nevertheless correspond to the same biochemical phenotype. The
apparent antiquity of the methanogenic phenotype plus the fact that it seems
well suited to the type of environment presumed to exist on earth 3-4 billion
years ago lead us tentatively to name this urkingdom the archaebacteria.
Whether or not other biochemically distinct phenotypes exist in this
kingdom is clearly an important question upon which may turn our concept
of the nature and ancestry of the ﬁrst prokaryotes.”

Propose “three aboriginal lines of descent”
! Eubacteria
! Archaebacteria
! Urkaryotes


Conclusion

“With the identiﬁcation and characterization of the
urkingdoms we are for the ﬁrst time beginning to
see the overall phylogenetic structure of the living
world. It is not structured in a bipartite way along
the lines of the organizationally dissimilar
prokaryote and eukaryote. Rather, it is (at least)
tripartite, comprising (i) the typical bacteria, (ii)
the line of descent manifested in eukaryotic
cytoplasms, and (iii) a little explored grouping,
represented so far only by methanogenic bacteria.”

Tree from Woese and Fox data

http://bioweb.pasteur.fr/seqanal/interfaces/neighbor.html

Woese 1987


26.23 Some Would Call It Hell; These Archaea Call It Home


70

Table 26.1 The Three Domains of Life on Earth


71

Table 26.1 The Three Domains of Life on Earth


72

26.22 Membrane Architecture in Archaea


74

Tree of Life

adapted from Baldauf, et al., in Assembling the Tree of Life, 2004


Most of the phylogenetic diversity of life is microbial

adapted from Baldauf, et al., in Assembling the Tree of Life, 2004


Simpliﬁed, Rooted Tree of Life


Alternative rooted tree of life

Archaea
Archaea


EVE161 Lecture 3

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