UNIT 3 - Chapter 11: Archaea

Horizontal Gene Mechanisms have significantly impacted...

microbial evolution

Selfish genes

parasitic DNA sequences that survive and reproduce but that do not increase the fitness of the host genome

Horizontal Gene Mechanisms have significantly impacted...

microbial evolution

Selfish genes

parasitic DNA sequences that survive and reproduce but that do not increase the fitness of the host genome

HGT has caused problems with using...

phenotyping to identify species of microbes

Lactose catabolism genes can be carried on...

plasmids that can be passed between species within different genera

16 rRNA and other molecular chromosomal markers with low mutation rates are needed for...

positive identification

16 rRNA mutation rate is....

0.02% every million years

used for identification of species

ex: 16s is 1600 bps so -> 1600 x 0.02 = 32 changes after a million years

Molecular marker

genes, portion of genes, or other genetic sequence used to identify and taxonomically categorize organisms and viruses

16 rRNA sequence is always used for

those organisms that have 70s ribosomes

16 rRNA sequence can be compared with millions of other sequences using...

BLAST software

Today's taxonomic identification is based on...

molecular markers and biocomputation using molecular marker sequence data

Four short sequences have been aligned, which is a way of arranging DNA, RNA, or protein sequences to identify regions of similarity.

Given these short pieces of 16s rRNA sequences, which two bacteria are most closely related?

A. Escherichia coli: 5' AUUCGCGAUC 3'

B. Proteus vulgaris: 5' AUGCGGGAAC 3'

C. Salmonella enterica: 5' AAUCGCGCGAUC 3'

D. Citrobacter freundii: 5' AUUGGCCAUC 3'

A. & D.

Why do archaea present a problem to the taxonomic organization?

most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples so they cause a disruption in the phylo tree

Archaea share features with...

eukaryotes AND prokaryotes

Archaea are extremely diverse in what ways?

physiologically

morphologically

Many but not all archaea are...

extremophiles

What are extremophiles?

organisms that grow under extreme conditions

What are examples of archaea extremophiles?

Thermophiles: hot springs in Yellowstone

Hyperthermophiles: oceanic volcanic vents

Barophiles: bottom of the ocean

Mesophiles: human gut; not extremophile

How do the chemical composition of Archaea cell walls differs from the cell walls of bacteria or eukaryotes?

Archaea cell walls do not have peptidoglycan

The key component is pseudomurein

The cells walls of Archaea are not affected by...

enzymes that breakdown peptidoglycan nor antibiotics that poison the synthesis of peptidoglycan

What are examples of enzymes that breakdown peptidoglycan or antibiotics that poison the synthesis of peptidoglycan?

Lysozyme (tears, saliva, food) breaks down peptidoglycan

Antibiotics that interfere with peptidoglycan synthesis have no effect on archaea

Why do gram stain patterns means nothing to archaea?

Because there is not peptidoglycan to stain in archaea

DIFFERENCES IN MEMBRANE LIPIDS (1)

In bacteria and eukaryotes, membrane lipids consist of...

straight chain fatty acids attached to glycerol by ester bonds

DIFFERENCES IN MEMBRANE LIPIDS (2)

In archaea, membrane lipids consist of...

hydrocarbon tails attached to glycerol by ether bonds

ether bonds are stronger so perform well in extreme environments

no fatty acids instead have saturated hydrocarbon chains with rings, making the cell walls more resistant to harsh conditions in extreme environments

What are Psychrophiles?

What are their membranes made up of?

cold-loving microbes

have unsaturated hydrocarbon tails with rings that do not stack

What are Hyperthermophiles?

What are their membranes made up of?

Heat-loving bacteria from 70-110 degrees Celsius

have saturated hydrocarbon tails, and cyclopentane rings that prevent leakage at high temperatures

Archaea membranes can be...

bilayers OR monolayers

What are monolayers?

more rigid and better able to resist harsh environments

prevents membranes from leaking

What are bilayers?

a thin polar membrane made of two layers of lipid molecules

What can Archaea do if they are faced with environmental changes?

they can modify their membranes

How do Archaea modify their membranes?

membranes are more open at lower temperatures, or higher pressure or higher pH

Membrances are less open at higher temperatures, or under lower pressure or lower pH

What similarities do Archaea have with bacteria?

Circular double stranded DNA genome and haploid polycistronic

Horizontal gene transfer, binary fission

Highly diverse metabolic pathways for energy production

What similarities do Archaea have with eukaryotes?

More than one origin of replication, similar replication proteins

Histones and nucleosome like structures

Introns

No sigma factors

Many translation factors, some share ribosome proteins

Archaea have two most well described phyla, which are....

Crenarchaeota

Euryarchaeota

Crenarchaeota

Archaea that live in extreme environments

examples: thermophiles, psychrophiles, acidophiles, extremophiles, S0 oxidizers & reducers

Euryarchaeota

the most diverse Archaea

examples: thermophiles, methanogens, acidophiles, halophiles, extremophiles, sulfate reducers

What type of relationship to thermophiles and acidophiles have in hot acid microbial mats?

symbiotic relationship

p.s. they both need sulfur

Sulfolobus

Thermoacidophile

Aerobic heterotroph: grows in hot acidic sulfurous springs

oxidizes sulfur: S0 to H2SO4

Thermoproteus

Thermoacidophiles

Anaerobic autotroph: grows in Hot acidic sulfurous springs

Reduce sulfur: S0 to H2S and fix carbon

What are the 5 major groups of Euryarchaeota?

more diverse than Crenarchaeota:

Methanogens

Halobacteria: Extremophile

Thermoplasms: Extremophile

Hyperthermophiles: Extremophile

Methanogens

stric obligate anaerobes

can break down cellulose

widespread in nature

habitat: environments rich in organic matter

What is the Ecological Importance of Methanogens?

Important in wastewater treatment

dangerous in landfills

produces significant amounts of methane

Halobacteria

no cell walls, only S-layer

extreme halophiles

aerobic respiration

pigments and high salt provide radiation protection

Extreme halophiles

require salt or will die by lysis

Rhodopsins

pigments that change configuration in response to light and trigger a reaction that stimulates nerves

Bacteriorhodopsin aka "visual purple"

Generates ATP from light energy

Purple membrane: aggregation of bacteriorhodopsin

Halorhodopsin

maintains intracellular concentrations of salts

Sensory Rhodopsins

photoreceptors

Control flagella ie. phototaxis

Thermoplasma

No Cell Walls, only S-layers

live in hot acidic springs

Extremely tough plasma membranes

Hyperthermophiles: Thermococcus kodakarensis

lives in Deep Sea Volcanic Vents

102C; so can grow above boiling

Has a reverse gyrase which makes DNA moreresistant to thermal denaturing

High transformation ability

Hyperthermophiles: Pyrococcus furiosus

rushing fireball

Optimum growth temp 88C to 110C

Has a reverse gyrase which makes DNA moreresistant to thermal denaturing

High transformation ability

Hyperthermophile: Archaeoglobus fulgidus

"ancient sphere" because it shines under UV fluorescent light at 420nm

Deep sea volcanic vents, high-temp oil deposits, & hot springs

Optimum growth at 83oC

No cell wall, S layer

Eukaryotic cells & bacteria cells have ___________ membranes

bilayer

Evolution of the Eukaryotic Cell