Diversity of Archaea

Diversity of Archaea

• Phylogenetic and functional diversity exist among primary groups of Archaea
• Evidence for archaeal diversity and biology comes from various sources

Korarchaeota

• These are uncultivated archaea
• They are hyperthermophiles
• Defined phylogenetically

Nanoarchaeota

• These are obligate symbionts
• They have small genomes

Euryarchaeota

• Includes thermophiles and hyperthermophiles
• Includes extreme halophiles
• Contains methanogens
• Some are non-methanogens such as Thermoplasma/Ferroplasma
  • These are acidophiles
  • They were obtained from coal refuse piles
• Marine Group II Euryarchaeota are relatives of Thermoplasma
  • Live in the open ocean
  • Planktonic archaea quantified via rDNA hybridization

Crenarchaeota and Thaumarchaeota

• The first discovered isolates were extremophiles (thermophiles/hyperthermophiles)
• Mesophiles also exist in this group
• Much of Crenarchaeota diversity is uncultivated
• Sulfolobus solfataricus lives in hot, sulfur-rich environments
• Pyrolobus fumarii has the highest temperature for life, 113°C
  • It lives in the walls of black smokers (hydrothermal vents)
• Marine Group I Crenarchaeota are thermophile relatives that live in the open ocean
• Thaumarchaeota are part of Crenarchaeota
• Ammonia-oxidizing archaea may be in Thaumarchaeota

Discovery of Ammonia-Oxidizing Archaea (AOA)

• 16S rRNA surveys showed abundant archaeal sequences
• Gene homologs of bacterial amoA (ammonia monooxygenase) were identified in archaea genomes
• Nitrosopumilis maritimus was the first cultivated AOA, performing autotrophic ammonia oxidation (nitrification)
• Cenarchaeum symbiosum is an extracellular ammonia-oxidizing symbiont of a sponge (Axinella mexicana)
• AOA are more abundant and efficient than AOB at low ammonia concentrations

Darwinian Threshold

• It's the transition from precellular to cellular life during the Last Universal Common Ancestor (LUCA)
• DNA replication, transcription, and translation are processes that cross the Darwinian threshold first
• Marks the transition from mostly horizontal gene transfer (HGT) to vertical gene transfer

Similarities Between Archaea and Eukaryotes

• Both share ribosomes for translation
• They contain homologs in:
  • Transcription machinery
  • ATP synthase
  • DNA polymerase

The Lipid Divide

• It represents uncertainty about the nature of the common ancestor
• Bacteria and eukaryotes have ester linkages in their lipids
• Archaea have ether linkages in their lipids
• Membrane evolution led to compartmentalization of cellular processes, including regulation of transport

Challenges in Microbial Eukaryote Systematics

• Issues exist with rRNA phylogenies
• Morphology doesn't always align with molecular systematics
• Discrepancies occur between phylogenetic markers, such as rRNA versus other genes
• Eukaryotic genomes have a chimeric nature
  • This is a mixture of organisms in the genome, especially for symbionts
• Lack of bootstrap support for supergroups

Asgard Archaea

• They were discovered in deep-sea sediments using metagenome-assembled genomes (MAGs)
• Contain eukaryotic signature proteins (ESPs), previously thought to be exclusive to eukaryotes
• They are the closest known relatives of eukaryotes
• Show more metabolic diversity than other eukaryotes

Roles of Microbial Eukaryotes in the Carbon Cycle

• Photosynthesizers fix carbon and turn it into rock
  • Protists form a shell that sinks into sediment, creating fossil carbon
• Predators exist
• Heterotrophs exist

SAR Group

• SAR is the most abundant group
• Stramenopiles have hairy flagella and include phototrophs and heterotrophs
  • Diatoms (phototrophs with shells)
  • Kelp (brown algae)
  • Oomycetes
• Alveolates are primarily parasites of humans and other organisms
  • They have sacs (alveoli) underneath the outer cell membrane
  • Dinoflagellates
  • Apicomplexa
  • Ciliates
• Rhizaria have some version of a shell
  • Amoeba

Anaerobic Eukaryotes

• Cannot perform aerobic respiration
  • Rely only on fermentation/substrate-level phosphorylation (SLP)
• Have atypical or no mitochondria
• Often possess hydrogenosomes

Primary Supergroups of Eukaryotes

• Opisthokonts
  • Includes animals, fungi, and choanoflagellates
• Amoebozoa
  • Have only amoeboid forms and actin-based motility

Types of Multicellularity

• Cohesive
  • Develops from a single progenitor cell via clonal division
  • Cells are physically attached
  • Forms a long-term multicellular body with specialized cells
• Aggregative
  • Cells aggregate temporarily in response to environmental cues or starvation
  • May separate later
  • Individual to multicellular/syncytial forms and differentiate into fruiting bodies
  • Disperse by spores/cysts

Bacterial-Eukaryote Symbiosis

• Endosymbiosis is common, but genetic fixation into organelles is rare
  • Nitroplast in marine algae was originally an endosymbiont that co-evolved with the host
• Symbioses shape the diversity of eukaryotes
  • Providing novel characteristics
• Symbiont genomes are reduced but control their replication, division, and expression
• Organelle genomes contain essential genes only, with division controlled by the cell
• Number of membranes indicates the number of endosymbiotic events
  • Primary: two membranes (host engulfs bacterium, retaining the bacterial membrane)
  • Secondary: three membranes (host engulfs cell with primary endosymbiont)
  • Tertiary: four membranes (host engulfs cell with secondary endosymbiont)

Hydrogenosomes

• Some eukaryotes lack mitochondria and don't need oxygen
  • Utilize fermentation/SLP
• Often have hydrogenosomes
  • Double membrane-bound organelles
  • Generate H2/CO2 and acetate (1 ATP), which is not energetically favorable alone
  • Syntrophy with methanogens pulls the reaction forward via interspecies hydrogen transfer
• Hydrogenosomes may have originated from mitochondrial reduction
  • Mitochondria to anaerobic mitochondria and then to hydrogenosomes

Mobile Genetic Elements (MGEs)

• MGEs transfer genetic material between hosts
  • Genetic material also persists within the host
• Plasmids mediate transformation/conjugation
  • They can be chimeric (mixtures of genomes from different hosts)
  • Encode genes for transfer and antibiotic resistance
  • Conjugative plasmids self-transfer using conjugation (tra) genes
  • They have oriT sequences for transfer initiation
  • Often carry antibiotic resistance genes (ARGs)
  • Mobilizable plasmids lack self-transmission genes
  • Can carry ARGs
  • Transfer occurs via "piggybacking" on conjugative plasmids
• Viruses mediate transduction
• Transposons mediate transposition
• Integrative and conjugative elements mediate conjugation
  • Function like plasmids crossed with transposons

Genetic Transfer

• Conjugation is cell-to-cell transfer requiring physical interaction
• Transduction is phage-mediated transfer
• Transformation is the uptake of genetic material from the environment

Plasmid Replication

• ori is the origin of replication with high A and T content
• Requires both host and plasmid proteins
  • repA is an initiator protein that nicks one strand
  • Host proteins include ligase and single-stranded binding proteins
• Rolling circle replication
  • repA nicks DNA at the origin
  • A new strand is synthesized continuously
  • The new strand is then cleaved and ligated

Accessory Genes

• Accessory genes are encoded on natural plasmids and cloning vectors
• Toxins/colicins, antibiotics, and cognate resistance genes
  • Producer is immune
• Virulence genes
• Degradative enzymes

Phage Components

• Structural components are a capsid, tail, and proteases
• Genetic components include lots of accessory genes

Viral-Host Interactions

• Lytic cycle
  • New viral particles are made, cell lyses, and releases progeny viruses
  • Horizontal transmission of phage genome into a new cell
• Lysogenic cycle
  • Virus integrates into the host genome, no production of new viral particles
  • Cell becomes a lysogen
    • The integrated phage is called a prophage
    • Is replicated with the host genome, enabling vertical transmission
  • Induction is activation of prophage to the lytic cycle

Host Cell Barriers

• Successful infection, i.e., no barriers
• Modification of virus receptor
• Degradation by restriction enzymes
• Modification of viral DNA
• Abortive infection by host cell
• CRISPR Cas system recognizes and degrades foreign DNA

Host Cell Defenses

• Host-encoded restriction enzymes cut viral DNA
  • Host methylates its own DNA for protection
• CRISPR-Cas9 system uses CRISPR spacers
  • Records of prior phage infections, providing adaptive immunity
  • Heritable, so uninfected cells can still be immune
  • Matches phage DNA, targeting a specific part of the phage genome

Giant Viruses

• Infect eukaryotes
• Are engulfed/eaten via phagocytosis
• Can reprogram eukaryotic hosts, providing a competitive advantage
• They are giant in size
  • Have large DNA genomes
• Contain translation components
• Assemble in viral factories, replicating in the cytoplasm
• Can be infected by virophages

Virophage

• Virus that can infect other viruses, brought in by a giant virus
• Can integrate into the host genome, providing defense against other viruses and increasing host cell survival

Transposons

• Contain terminal inverted repeats
  • When inserted, flanking direct repeats are obtained
• Transposase mobilizes transposons
  • Often encoded by the transposon itself
• Conservative transposition
  • (Cut and paste)
  • Transposon is excised from donor DNA
  • Inserts one copy into a different genome
• Replicative transposition
  • (Copy and paste)
  • Transposon is replicated
  • Donor DNA is undamaged
• Transposon-based mutagenesis
  • (Random)
  • Uses transposons to create mutants, enabling selection of different mutant phenotypes
• Conjugative transposons carry genes for conjugation
  • Excision from donor DNA leads to conjugative transfer to the recipient cell where it integrates
  • Enable both mobilizable plasmids and non-conjugative transposons to be transferred via conjugation

Spore Formation

• Endospores are formed only in Firmicutes (Bacillus and Clostridium)
  • Bacillus thuringiensis has an endospore coat that contains insecticidal proteins
  • Can be sprayed onto plants or used for genetic engineering
• Sporulation occurs only when limited or no options
  • Requires sensing of environmental conditions, nutrient deprivation, and population density
  • Checkpoints ensure all other options are exhausted
  • Cells are committed once sporulation starts
  • Spo0A is the deciding factor, becoming phosphorylated as signals accumulate
  • Chromosome stretches out and asymmetric cell division begins, generating a mother cell and forespore
  • Mother cell engulfs the forespore, which continues developing inside its mother cell
  • Requires coordinated gene expression in the forespore and mother cell
  • Mother cell supports the forespore, but ultimately dies, releasing the spore
  • The result is metabolically inactive and partially dehydrated, with components in the core
  • Calcium dipicolinate enables heat resistance
  • SAPs (small acid-soluble spore proteins) store and protect DNA and are an energy source during germination
• Streptomyces spores are formed by Streptomyces growing in filaments
  • Older filaments lyse as nutrients run out to produce antibiotics
  • Aerial mycelia grow and produce spores at their tips
  • Used for reproduction and dispersal
  • Metabolically active, but less resistant than endospores
• Myxospores are formed by myxobacteria upon starvation
  • Aggregate and form fruiting bodies containing myxospores
  • Less tough than endospores
  • Only formed when it's the last option and not for dispersal

Unique Life Cycles

• Metabacterium polyspora is an endospore former in Firmicutes that inhabits guinea pig GI tracts
  • Sporulation is tied to the timing of passage through the GI tract
  • Guinea pigs ingest feces with spores, which germinate in the upper intestine
  • More spores are produced, and then released in feces
  • Spore formation becomes the primary reproductive mechanism
  • Forespore forms at the poles and can do binary fission
  • Endospores immediately germinate inside the mother cell
• Epulopiscium reproduces via production of multiple live offspring
  • This is also the only method of reproduction
  • The mechanism is similar to sporulation, but never forms spores
    • Mother cell lyses

Caulobacter

• Cell division occurs via unequal binary fission
• Has a dimorphic life cycle
  • Motile swarmer cells are chemotactic dispersal forms that do not replicate
  • Stalked cells
    • Cannot revert back to swarmer cells
    • Can divide and make new swarmer cells
    • Stalk length is inversely correlated with nutrient concentration, especially phosphate
      • Longer stalk allows larger surface area and better nutrient uptake

Bacterial Motility

• Requires a motility apparatus and sensory system
• Swimming motility is flagellar or non-flagellar
  • Bacterial flagella have a helical rotary structure like a propeller
  • External except in spirochetes
  • Powered by PMF (similar to ATPase)
  • Must be constantly rebuilt because when the flagella whips around, part of it breaks off
  • Overall conserved in all bacteria, but with some small variations
    • Flagellum proteins self-assemble, starting with the basal body and rod and then the hook assembly and filament
    • The cell only makes flagella when outside the cell because self-assembly can occur within the cell
    • Flagella are often upregulated in nutrient-poor conditions
• Surface motility with type IV pili in Pseudomonas aeruginosa allow twitching motility
  • Extend, attach, and retract
  • Powered by ATP
• Myxococcus exhibits A-motility
• A form of gliding motility where cells move independently
• Form focal adhesions to surfaces and push
• Move forward by forming adhesions at the front edge while disassembling at the back
• Is a social has type IV pilus that allows cells to move together

Filamentous Cyanobacteria

• Movement with mostly pili, some gliding

Unicellular Cyanobacteria (Synechococcus)

• Movement with gliding and focal adhesions

Flavobacteria

• Movement with gliding and focal adhesions

Bacterial Flagellar Motility

• Acts as a corkscrew propeller
• CCW rotation allows cells to move forward
• CW rotation allows the cells to tumble (random)

Archaeal Motility

• Archaeal flagella (archaellum) components are homologous to type IV pili
• Rotate as bundles
• Do not extend and retract
• Chemotaxis system proteins (e.g., MCPs) are conserved in bacteria and archaea
• Haloarchaea can be motile and phototactic
• Use sensory rhodopsins to sense light wavelengths
• Light wavelength influences swimming behavior

Spirochete Motility

• Flagella located in the periplasm: "endoflagella"
  • Wrapped around the cell body, giving it a helical shape
• Flagella at each end must rotate in opposite directions
  • Allows it to swim forward/backwards
  • Same direction = flexing
• Advantages
  • Allows for movement in viscous liquids
  • Flagella are protected
  • The cell prevents eliciting an antigenic response

Bacterial Chemotaxis

• Switching from run to tumble
• Controlling the frequency of the switch allows for chemotaxis which is more movement
  • If moving towards attractant, extend runs
• Machinery
  • Attractants (nutrients)
  • Repellants (toxic compounds)
  • Chemosensory array at cell end
  • Have MCPs (methyl-accepting chemotaxis proteins) that senses by having sensory domains
  • MCPs have output domains where it the monitor sensitivity based on its methylation
  • CheA which is histidine kinase
  • It integrates the signal from the MCPs
  • CheY is a response regulator for flagellar motility
  • Takes a lot of the input and directs it to the response
• Magnetotaxis increases efficiency of aerotaxis
• Magnetotaxis is passive
  • Cells are pulled into magnetosomes which are membrane-enclosed structures containing magnetic mineral act as compass needle'to align by magnetic minerals
  • Reduces search space

Quorum Sensing

• Cell density-dependent regulation that allows bacteria to monitor their population and respond accordingly
• Can enable interspecies communication
  • Autoinducers are shared across species
• Some examples include
  • Bacterial luminescence
  • Reaches a population threshold and flips switch for luminescence
  • Each cell produces a signaling molecule
    • Example is, Aliivibri fischeri in symbiosis with Hawaiian bobtail squid where Aliivibrio gets protection and nutrient supply
      • The quid development depends on colonization because Vibrio alters their host gene expression
      • Host receptors detect specific symbiont chemicals
      • Host organisms make specific antimicrobials to rid get rid of potential colonizers
      • Luminescence genes can be transferable to other species
• Pathogenesis
  • For example in P. aeruginosa which forms biofilms by being protected by exopolysaccharide matrix
  • They are also then resistant to antibiotic treatment
• Quorum sensing may also contribute towards biofilm production and finally virulence factor production via Las and Rhl systems
  • Las controls Rhl and produces the 2nd autoinducer
  • Proteins are homologs of LuxI/LuxR
  • LasR/I mutations cause defective biofilm formation
  • Mutants lacking LasR/I and/or RhlR/I causes decreased pathogenicity
  • Why induce this virulence factor and promote biofilm production at a high cell density
  • You don't want to trigger an immune response unless you have enough competent cells
• It can target the quorum sensing signals for treatment therapies

Lumeniscence

• Genes for luminescence are highly controlled
  • Is very expensive
  • 50 ATPs is what you need to produce the one photo of light
  • Involves production and detection of a diffusible small molecule
  • Positive feedback loop
  • The LuxI protein synthesizes the autoinducer
  • Diffuses into the medium
  • At a threshold concentration, you autoinducer gets diffused back into the cell
  • Causes Autoinducer to bind with LuxR to activate the lux transcription
  • That becomes light production