Integrative Bio 43 MIDTERM I

uc berkeley

what do aphids depend on buchnera for?

essential aminmo acids (10-20) and some vitamins

what are buchnera to aphids?

obligatory endosymbionts

where do buchnera live

in aphid bacteriocytes

what are obligatory endosymbionts?

organisms that live entirely inside the cells or body of a host organism and cannot survive or reproduce independently outside of that host

what do buchnera get from aphids?

carbohydrates/energy

mutual dependence leads to co-evolution which leads to _____________

mutual adaptations

what is the genomic adaptation in buchnera and what is the result on the genome in aphids

• genomic adaptation: huge gene loss (different species can lose different genes —> different species see different patterns of gene loss depending on the environment and what’s needed)

• genome expansion in aphids, possibly to enable better collaboration with the symbiont (ex: duplicating the # of amino acid transporters)

where do aphids get their carbohydrates from

plant sap

how are buchnera propogated thru generations if buchnera can now no longer live without aphids?

buchnera are vertically transmitted

whats vertical transmission

mother → offspring

how do mothers pass on buchnera to their offspring

the proximity of the uterus and the place where the embryos develop → buchnera is expelled from bacteriocytes and taken up by the embryos

when the hatchings come out of the mother, they are already populated with good symbionts that will help them properly develop and become a reproductive adult

define speciation

the evolutionary process by which new and distinct specifes develop from existing propulations

define co-speciation

when two groups of organisms undergo parallel speciation

what can mutual dependence and co-evolution lead to?

co-speciation

whats a phylogenetic tree

the story of how a group of organisms has evolved and their relationships

congruent trees of aphid and buchnera evolution show _____________, signifying that their interactions were a dominant factor in shaping their evolution

co-speciation

example of extracellular symbiont and how it works

platapsid stinkbug and Ishikawaella capsulatum —> mother stinkbug lays 4 eggs and then deposits a capule of the symbiont and when each pair of 4 eggs hatch, they go and eat that capsule so that they can intake the symbiont.

the symbiont lives in the stinkbug’s gut

what can gene loss and reduced variation in symbionts lead to?

evolutionary dead-end

• isolation = reduced gene variation

• cannot provide novelty to help host in a changing environment

• dwindling metabolic capabilities/degeneration

• reproduce faster

what can aphids do if their symbionts may drift toward degeneration?

make use of a secondary symbiont

what is a secondary symbiont also called

facultative symbiont

whats a facultative symbiont?

an organism that lives in a close relationship with another species, but does not strictly require that relationship to survive or reproduce

how can an aphid’s facultative/secondary symbionts be transmitted?

vertical and horizontal transmission

where may aphid secondary/facultative symbionts inhabit?

• bacteriocytes

• haemolymph (insect blood)

• other areas potentially

why are secondary/facultative symbionts useful in aphids?

• can complement synthetic pathways lost in buchnera/compensate for losses in buchnera

• can also offer additional diverse services/ services of local relevance

what is one specific example of a secondary symbiont to aphids?

serratia:

• often taken as a secondary symbiont to compensate for metabolic capabilty losses in Buchnera

• some cases have moved from facultative to co-obligate

  this means some aphids must have both buchnera and the serratia symbiotica

what does facultative ricketsiella & hamiltonella do for aphids?

production. of aphid pigments (turns them green and ladybugs prefer red aphids)

what does hamiltonella defense do?

prevents wasp larvae from developing and killing the aphid

different H. defensa strains are useful against different wasps

what is H. defensa protection of aphids the outcome of?

horizontal gene transfer mediated by phages (transduction)

what did sequencing of the Hamiltonella denfensa genome+ indentify?

• one chromosome and 2-3 conjugative plasmids

• at least 2 prophages, one of which was named APSE

what does the APSE prophage encode for?

often encodes toxins

• Shiga toxin → e. coli deaths are caused by this toxin

• CdtB - cytolethal distending toxin

these can kill thr growth of the wasp larvae within the aphid

what are conjugative plasmids

• small circular genetic elements

• transmitted between bacteria of the same generation

• transmitted by the process of conjugation

• involves pilli

what are prophages

viral DNA integrated into the host genome

why dont ALL aphids have H. defensa if it provides such a benefit to aphids?

because some environments dont have black wasps

cost & effect

there is a cost (lower reproductive success) of hosting the symbiont… so without the wasps un the environment, its not beneficial to host the symbiont

what lives inside us?

1. bacteria (100 trillion)

2. archea (400 billion) (0.4-0.8%)

3. fungi 100 billion (0.1%)

4. protists 100 billiion (0.1%)

5. parasitic worms (common in low income countries)

6. viruses 1 trillion particles

1. bacteria

2. archea

3. fungi

4. protists
   what is common about all of these?

all are unicellular

what is the rumen

one of the compartments of the stomach of many herbivores such as cows, sheep, deer, buffalo

why do herbivores need microbes

animals don’t have the enzymes to break down plant material (plant cell walls)

whats is cellulose made of?

glucose

what are sugars

saccharides, carbohydrates

how many microbes does the rumen have?

10^15 - 10^16

whats inside the rumen (conditions)

no oxygen (anaerobic) and very slightly acidic pH 6, 39°C

define ecosystem

a community of living things working together with the non-living parts of their environment

list the chain of how plant matter is turned into energy for the host

1. plant polysaccharides

2. bacterial fermentation

3. volatile fatty acids

4. absorption by the rumen epithelium

5. host energy

what are plant complex polysaccharides digested by?

cellulolytic bacteria, fungi, protists

what is released after cellulollytic microbes digest plant polysaccharides

simple sugars

how are cellulolytic microbes able to break down polysaccharides

they release enzymes that are able to break the polysaccharides and that releases sugars

what is functional redundancy

multiple different parts, species, or systems perform the exact same job or role

what happens in rumens metabolism after simple sugars are released

anaerobic fermentation

whats released by anaerobic fermentation

VFAs (acetate, butyrate, proprionate) → volatile fatty acids
CO2

H2

what, ultimately in the rumen’s metabolism is energy for the host and what is energy for microbes?

VFA (voltile fatty acids)is energy for the host
energy for the microbes consist of CO2 and H2
Methanogenic Archea turn the CO2 and H2 into methane which is burped out (CH4)

whos mostly responsible for creating hydrogen in the rumens metabolism

protists

what does high butyrate do for a cow?

high milk yield

what does a low quantity of protists do for a cow

lowers H2 and thus lower methane production

gram + bacteria

• thick peptidoglycan layer (cell wall)

• lipid bilayer (cell membrane)

gram - bacteria

• lipopolysaccharide (LPS)

• peptidoglycan

• lipid bilayer (cell membrane)

archea cell wall & membrane structure

• cell wall (pseudo-murein)

• cell membrane (different lipids)

what is and whats the prupose of flagella

• acts as a rigid rotor to achieve movement rates of up to 100 body lengths/second

• propelling, motility

what is the flagella made of?

self assembling machine made of ~50 proteins

what is fimbriae used for

adhesion

What are pili used for?

• conjugation

• enable attachment (to surfaces or cells)

• secretion of toxins

What is conjugation

allows for horizontal gene transfer

involves the transfer of a plasmid from one cell to another, encoding the proteins of the pilus itself + genes for goodies (e.g. antibiotic resistance, toxins)

what different things full under the category of eukaryotes

• animal cells

• protists

• fungi

• plant cells

qualities of eukaryotes

• membrane-bound organelles

• internal membrane systems (endoplasmic reticulum, golgi, etc)

• A net of fibers forming a cytoskeleton

• larger than bacteria (10-100x in diameter)

• cannot replicate as fast as bacteria (every 20 min)

• fungal and plant cells have outside the cell membrane an additional cell wall

microbiome

all the genomes of microbes in a community

microbiota

community of microbes

in our gut, viruses are almost exclusively _________ (type of virus)

bacteriophages

why are viruses not considered organisms

• cannot replicate independently

whats a virus

a genetic element that can multiply only inside a living cell (the host cell)

whats a VFA

volatile fatty acids
Produced as a waste product of microbial anaerobic fermentation

• Major examples: acetate, butyrate, propionate

• The cow absorbs VFAs and uses them as a major source of energy.

• They may also be called short-chain fatty acids (SCFAs)

chemotaxis

Directed movement in response to a chemical gradient

what is phage specificity and why does it occur?

phages generally infect particular bacteria and must recognize and bind to a specific cell-surface receptor before infection

if the receptor isnt compatible, the phage cannot successfully infect that bacterium

steps of the lytic cycle

1. attachment: phage binds to a receptor on the bacterial surface

2. injection: phage injects its DNA into the bacterial cell

3. replication: the phage DNA takes advantage of the bacterium’s cellular machinery

4. viral gene expression: the host produces phage proteins

5. assembly: new phage particles are assembled inside the bacterial cell

6. lysis: the bacterial cell breaks open

7. release: new phages escape and can infect additional bacterial cells

   1. Attach → injection → replication → assembly → lysis → release

   2. AIR ALR

steps of the lysogenic cycle

Instead of immediately reproducing and killing the bacterium, the phage DNA integrates into the bacterial chromosome.

Phage infects bacterium

↓

Phage DNA enters

↓

DNA integrates into bacterial chromosome

↓

PROPHAGE

↓

Bacterium replicates normally

↓

Prophage DNA is replicated along with bacterial DNA

how does a phage switch from the lysogenic cycle to the lytic cycle?

If the bacterial host experiences serious stress, particularly DNA damage, the prophage may switch into the lytic cycle.

if the host cell is likely to die, remaining inside that cell is no longer advantageous for the phage.

the switch from lysogenic to lytic goes like:

DNA damage in bacterial host

↓

Host activates DNA-damage/repair responses

↓

Prophage detects/responds to these conditions

↓

Phage DNA excises from chromosome

↓

Phage enters lytic cycle

↓

Replication + assembly

↓

Cell lyses

↓

Phages escape

what are bacteria’s immune mechanisms?

CRISPR
CRISPR originally functions as part of a bacterial defense/immune mechanism against foreign genetic material, including bacteriophages.

how does CRSPR work in bacteria?

1. phage injects foreign DNA

2. CRISPR-associated defense recognizes/targets foreign genetic material

3. foreign DNA is cut/destroyed

4. Phage infection can be prevented

what is transduction and how does it work?

• another major example of horizontal gene transfer

• sometimes where prophages exit, it is excised incorrectly and accidentally takes adjacent bacterial DNA with it

• that phage can the infect another bacterium and transfer that bacterial gene

what are examples of what the tranferred gene (thru trhansduction) may encode?

• metabolic capabilities

• antibiotic resistance

• other useful functions

why do phages matter to bacterial evolution?

• give bacteria new genes

• give bacteria new metabolic functions

• spread antibiotic resistance

• accelerate bacterial evolutionary change

• However, gene transfer is not completely unrestricted because phages have host specificity.

what is cross-feeding

Products from one organism are used by another

fermentation

anaerobic metabolic process used by rumen microbes to obtain energy

prokaryote

cell without a membrane-bound nucleus

methanogen

archaeon that produces methane

hygiene hypothesis

Hypothesis linking reduced historical microbial/parasite exposure with altered immune regulation

gram + vs gram -

Gram+ = thick peptidoglycan.
Gram− = thin peptidoglycan + outer membrane containing LPS.

lytic cycle in short

Phage infects → replicates → assembles → lyses bacterium

lysogenic cycle in short

Phage DNA integrates → prophage → copied with bacterial genome → can later switch to lytic.

transduction

Phage accidentally carries bacterial DNA → infects another bacterium → transfers bacterial genes.

what is fitness focused upon

• An organism that survives but never reproduces has fitness = 0.

• Evolution acts on traits that are passed to future generations.

• Therefore, fitness is essentially about an organism's contribution to the next generation's gene pool.

where did mitochondria come from

Mitochondria evolved from an ancient bacterial endosymbiont.

what is mitochondria’s origins supported by?

1. own genome

2. ribosomes

3. replication

4. membranes

5. bacterial similarities

what happened to most ancestral mitochondrial genes

lost or transferred to the host genome

what is coevolution

occurs when interacting species evolve in response to one another

why are biological environments called moving targets

because interacting organisms themselves evolve

whats a major benefit of mutualistic symbiosis? (give an example)

the ability to open new niches — the ability to exploit resources that would otherwise be unavailable

Symbiosis → access to new resource → new niche → reduced competition

Mojave desert wood rat

• Eats toxic creosote.

• Symbionts help it tolerate/process this resource.

• Allows the animal to use food that competitors cannot.

whats a bacteriocyte

specialized host cell containing bacterial symbionts

whats a bacteriome

groups/tissues containing bacteriocytes

whats an obligate endosymbiont?

They cannot survive independently outside of the host.

endo = inside