Bacteria and Archae introduction

Question 1

How can the tree of life be made using rRNA?

Answer 1

Compare the primary sequence of rRNA for 16s small ribosomal subunit - common to all life.

Sequences of 16s rRNA is highly conserved amongst different organisms, but different enough to be able to group them.

Question 2

What is the most probable tree of life nowadays?

Answer 2

LUCA does not appear to be probable:
Rather a net of prokaryotic organisms with high rates of Horizontal Gene transfers (HGT) as ancestors to all living organisms.

Current bacteria and Archaea result from many HGTs within, and between these two groups.

Eukaryotes originated from these two groups - with initial archaea-bacteria fusion, HGTs, and acquisition of new organites through endosymbiosis of cyanobacteria.

Question 3

What is the hypothesis of origin of eukaryotes?

Answer 3

Initial archaea-bacteria fusion, many HGTs, and acquisition of new organites through endosymbiosis of cyanboacteria.

Fusion of ancient bacteria and archaea, with evolution of mitochondria endosymbiosis to acquire new organites.
- With evolution towards LECA - Last eukaryotic common ancestor.

Question 4

What were the Koch postulates?

Answer 4

Micro-organisms present in diseased host, but not in healthy person.

Isolated micro-organism injected into healthy person should cause illness.

The micro-organism should be then be able to be istolated from newly infected person.

Question 5

What is Bergey’s manual for defining species of Archaea/Bacteria?

Answer 5

Species:
Group of strains with major organisational resemblances and distinctive characteristics from others.

DNA-DNA homology more than 70% between strains.

Less than 5 degrees C difference in DNA melting temperature.

97+% rRNA sequence similarity.

Question 6

What are the different shapes of bacteria vs archaea?

Answer 6

Bacteria:

Coccus - sphere
Bacillus - rod
Vibrio - spiral
Filament
Pedunculate - extremities with different shapes.

Archaea:
Tubers - Prydoctyium
Bacillus - Thermoproteus
Irregular = Triangular = Haloarcula.

Question 7

Why is bacterial morphology important?

Answer 7

Escape predation by adapting cell shape and size - to prevent amoeba digestion.

Environmental conditions impact morphology - biofilm formation.

Antibiotic vulnerability - changing SA will change antibiotic accessibility.

Nutrient availability is greater with larger shape, but also more prone to predation.

Question 8

How do bacteria and archaea compare to eukaryotes by size?

Answer 8

Eukaryotic - 10-100 microns.

Bacteria - 1-10 microns.
(3 microns long).

Archaea 0.1-5 microns

bacteria tend to have greater diversity, and larger.

Question 9

What are found within bacterial cytoskeletons?

Answer 9

Protein filaments homologous to those of eukaryotes.

Lack many regulators of polymer dynamics.

Homologs to ACTIN:
MreB and ParM.
(CELL SHAPE)

Homologs to TUBULIN:
FtsZ
(DIVISION)

Question 10

What proteins are involved to determine bacterial cell shape?

Answer 10

MreB (typically absent) in coccus.

MreB is ATPase.

VERY important in Rod-Shaped.

MreB interacts with peptidoglycan elongation holoenzyme complex.
= Elongasome complex.

MreB patches interact with elongation holoenzyme complex causing the PG monomers to assemble together in helical paths.
= Rod-Shaped.

MreB guides the synthesis, but PG is still main determinant.

Crescentin involved to form Crescent-rod shapes.
= mReB controls deposition of Crescentin (Which has reduced PG synthesis)

Question 11

What proteins involved in bacterial cell division?

Answer 11

FtsZ polymerises in the centre of bacterial cells undergoing cell division:
Formationof Z-Ring.

Min proteins inhibit the polymerisation of FtsZ at the cell poles, allowing for nucleoid occlusion.

ParM is an actin homolog, which segregates bacterial chrosomes.

Question 12

How can you inhibit bacterial cell shape determination?

Answer 12

Apply A22

A22 inhibits MreB function.

MreB can therefore not interact with peptidoglycan synthesising enzymes to form helical peptidoglycan paths and drive rod shape.

Question 13

How can you inhibit FtsZ?

Answer 13

Many inhibitors of FtsZ, such as CCR-11.

With CCR-11, FtsZ is unable to form Z-ring and cause nucleoid occlusion.
Therefore, cells may undergo mitosis, but fail to cytokinese, forming long chains, with many nucloeids.

Question 14

What are cytoskeletal proteins in Archaea?

Answer 14

Homologs to Actin:
Crenactin.

Homologs to Tubulin:
CetZ.

Also found, MreB like in bacteria.

Question 15

What are regulators of polymer dyanmics?

Why important?

Answer 15

Can regulate dynamics of actin or tubulin polymerisation.

Profilins can regulate polymerisation of G-actin to F-actin.

Bacteria lack many regulators of polymer dynamics.

There is proximity of profilins between archaea and eukaryotes, to strengthen the idea of proximity of these organisms.

Question 16

What are similar to eukaryotic cytoskeletons?

Answer 16

Archaea cytoskeleton much closer to eukaryotes than bacteria are.

Suggests Eukaryotic cells evolved from endosymbiosis of archaea and bacteria?

There are many more homologs to eukaryotic cytoskeletal proteins in Archaea than in bacteria.

Actin and Crenactin (archaea) are more similar in structure.

mReB, ParM are more dissimilar (But both in bacteria and archaea)

Regulators of polymer dynamics proximity to eukaryotes and archaea suggest evolutionary proximity.

Question 17

What are Inclusion Bodies?

Answer 17

Storage granules:

Organic/Inorganic
Membrane-free/Enclosed in membrane.

Organic inclusion bodies are always enclosed with a membrane, whereas inorganic can be or not.

Question 18

What are inorganic inclusion bodies?

Answer 18

Membranes:

Magnetosomes enclose Iron globules = Aquaspirullum magnetotacticum.

Sulfur granules - for H2S use as electron donor in photosynthesis, and NO3-/02 as electron acceptor.
= In chemoautotrophic bacterium mm in diameter!

Non-membrane:

Polyphosphate granules = as a store of phosphate.

Question 19

What are organic inclusion bodies?

Answer 19

Store within membrane enclosed:

Glycogen - for glucose starved conditions.

PHB - appear under oxygen deprivation.

Question 20

How can photosynthesis not be oxygenic?

Answer 20

Photosynthetic bacteria are not always oxygenic!

Sulphurous bacteria use light energy to oxidise H2S, not water.
Produce solid sulfur (S), deposited in granules within cells.

= Found in hot springs.

Question 21

How can bacteria be magnetic?

Answer 21

Magnetotactic bacteria

Contain Magnetosomes = Membrane enclosed, inorganic inclusion bodies.

Containing iron globules

MamK (MreB/actin homolog)invaginates PM to form magnetosomes.
= Cytosekeltal proteins used to position organelles within cells.
= MamK used to position magnetosomes within cell.

Able to move in response to magnetic line.

Question 22

What is the nucleoid?

Answer 22

Cytoplasmic found.

Contains mostly supercoiled DNA, RNA and proteins.

Nucleoid contains usually a single, circular chromosome + plasmid(s).

Chromosomes are circular, with dsDNA, with topoisomerase proteins for supercoiling and Hu proteins (BUT NO HISTONES)

Question 23

How is bacterial DNA compacted?

Answer 23

Bacterial DNA is much longer than length of bacteria.
= Must be compacted.

But needs to remain accessible to transcription and replication, regulation.

Condensed through association with Hu proteins, and supercoiled with Topoisomerases.

DNA loops start from a more condensed point.

Question 24

How is bacterial DNA arranged?

Answer 24

The nucleoid contains a central zone, which is highly condensed, inactive genes, with DNA loops extending.

No membrane for nucleoid.

DNA supercoiling with topoisomerases and Histone-Like proteins.

Highly variabel chromosome sizes between species - less than 5000kbp in E.coli.

Question 25

What are the functions of chromosomes?

Answer 25

Major repository of genetic info - replication to transmit genetic characteristics.

Code vital functions via gene expression through transcription

Question 26

How are bacterial DNA replicated?

Vs archaea?

Answer 26

Semi-conservative process, whereby one strand is used as template to synthesise complementary strand.

Bidirectional from a single Origin = Bacteria.

Bidirectional from 1 or more origins in Archaea.

Origins are rich in A and T bases.

Semi-discontinous replication.