Download Endosymbiosis: The Evolution of Metabolism

Endosymbiosis: The Evolution of Metabolism
In eukaryotic cells:
Why is oxidative phosphorlylation (most of ATP synthesis) done in the
mitochondria?
Why is the light reaction of photosynthesis done in chloroplasts?
Chloroplasts and mitochondria are peculiar organelles. They have double membranes
and their own circular DNA molecules. They also reproduce independently of the cell.
In 1965, Dr. Lynn Margulis proposed the theory of Endosymbiosis. She claimed that
mitochondria and chloroplasts are actually descendants of ancient bacteria that were
captured by the ancestors of eukaryotic cells more than a billion years ago.
- Endosymbiosis is clearly a crazy theory, isn’t it?
- What is the evidence?
Margulis presented several types of physical evidence to support her theory.
1) Mitochondria and chloroplasts have their own DNA
2) Mitochondria and chloroplasts reproduce independently of the cell
3) Mitochondria and chloroplasts have membranes that are not connected to other
cellular membrane systems
4) Cases of Endosymbiosis can be found in present day organisms such as Chlorella
alga inside of Paramecium
This argument was not sufficiently persuasive and most scientists rejected the
Endosymbiosis theory when it was first presented. However, in the early 1980’s Dr.
Margulis was able to use DNA sequence analysis (bioinformatics) methods to validate
the endosymbiosis theory.
She compared gene sequences between mitochondria and bacteria; and also between
chloroplasts and blue-green algae (photosynthetic bacteria). You can re-create her
experiments using sequences from GenBank and the BLAST sequence similarity tool
at the NCBI website (see the Sequence Similarity Tutorial in Appendix B).
Start with genes from the mitochondria. What genes are in a mitochondrion? It has a
small genome – just 16,000 bases in humans with about 20 genes. Which of these
genes are likely to remain essentially unchanged over a few billion years?
Respiration - specifically the Krebs cycle is highly conserved.
succinate dehydrogenase is a good choice
[Note: It is easier to find distant similarities if we use protein sequences rather than
DNA sequences to make similarity searches.]
So, use a web browser to get the succinate dehydrogenase gene sequence for human
mitochondria from Genbank. GenBank is an online database which contains all
known DNA and protein sequences. It is run by the NCBI (National Center for
Biotechnology Information), which is part of the US National Library of Medicine at
the NIH:
http://www.ncbi.nih.gov
Or just do a Google search for “GenBank”.
Q uickTim e™ and a
TI FF ( LZW) decom pr essor
ar e needed t o see t his pict ur e.
Who owns GenBank and the data in it? We all do – both GenBank and the sequences
in it are paid for by US tax dollars allocated by congress for scientific research at the
NIH and Universities across the country. Other sequences are contributed by scientists
from all over the world, as a requirement for publishing articles in respected Journals.
Europe and Japan maintain their own DNA sequence databases (EMBL and DDBJ),
but they exchange sequences with GenBank every day, so that all three databases
contain all of the same information. GenBank also includes data imported from other
databases such as SwissProt and PIR. The proteins records from SwissProt are
particularly valuable because they have more thorough and extensive annotation, and
they have much less redundancy (duplication) than the rest of GenBank
Open the NCBI website and type your search terms directly in the “Search” box near
the top of the page. Use the pulldown menu to set the search for Protein. It may take
a while to locate the correct succinate dehydrogenase gene if you try to search
GenBank with text terms:
[“succinate dehydrogenase” + human + mitochondria + subunit 2]
GenBank is very big (over 2 million proteins in 2004), and the gene names are not
very well organized. The Entrez search engine is very powerful, but not terribly easy
to use. One shortcut is to use the locus name: DHSB_HUMAN, or the accession
number: P219912.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Once you find the human mitochondrial succinate dehydrogenase gene, click on the
link and have a look at the GenBank record. There is a LOT of information here
including keywords, pointers to other GenBank records and cross-references in other
databases.
LOCUS
DEFINITION
ACCESSION
VERSION
DBSOURCE
KEYWORDS
SOURCE
ORGANISM
REFERENCE
. . .
P21912
280 aa
linear
PRI 25-OCT-2004
Succinate dehydrogenase [ubiquinone ] iron-sulfur protein,
mitochondrial precursor ( Ip) (Iron-sulfur subunit of complex II).
P21912
P21912 GI:20455488
swissprot : locus DHSB_HUMAN, accession P21912;
class: standard.
extra accessions:Q9NQ12,created: May 1, 1991.
sequence updated: Feb 28, 2003.
annotation updated: Oct 25, 2004.
xrefs : gi: 665924, gi: 665925, gi: 773298, gi: 773300, gi: 773291,
gi : 773292, gi: 773293, gi: 773294, gi: 773295, gi: 773296, gi:
773297, gi: 5263031, gi: 8979800, gi: 33871966, gi: 14043765, gi:
220069, gi: 220070, gi: 180916, gi: 180917, gi: 7431697
xrefs (non-sequence databases): HSSPP07014, GenewHGNC :10681,
ReactomeP21912, MIM 185470, MIM 115310, MIM 171300, MIM 171350,
GO0005739, GO0009060, GO0006099, InterProIPR006058,
InterProIPR001450, InterProIPR004489, InterProIPR001041,
InterProIPR009051, PfamPF00111, TIGRFAMsTIGR00384, PROSITEPS00197,
PROSITEPS00198
2Fe-2S; 3Fe-4S; 4Fe-4S; Disease mutation; Electron transport; Iron;
Iron-sulfur; Metal-binding; Mitochondrion; Oxidoreductase ; Transit
peptide; Tricarboxylic acid cycle.
Homo sapiens (human)
Homo sapiens
Eukaryota ; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi ;
Mammalia ; Eutheria; Primates; Catarrhini ; Hominidae ; Homo.
1 (residues 1 to 280)
Use the Display pulldown menu to show just the amino acid sequence of the protein in
“FASTA” text format. Copy the amino acid sequence. Now go to the NCBI BLAST
web page and choose “Protein-Protein BLAST.” Paste the DHSB_HUMAN amino
acid sequence into the Search box. Choose “swissprot” from the Choose Database
pulldown menu and click the nice big _BLAST!_ button.
Q uickTim e™ and a
TI FF ( LZW) decom pr essor
ar e needed t o see t his pict ur e.