Microbiology Exam 3 Flashcards
Lederberg 1946
Used auxotrophic strains of E. Coli to study gene transfer
Had to have direct contact for gene transfer
Said it was sexual reproduction which is wrong, it was conjugation
Conjugation
DNA is transferred from one cell to another cell
Needs direct contact
Cells are connected by pilus structure
DNA transfer is directional donor cell to recipient cell
Plasmid
Replicate independently from the bacterial chromosome
F-plasmid
Has genes so it can replicate independently
Has origin of replication
Has genes (tra region) for conjugation to occur
What happens during conjugation?
F+ pilus connects to F- cell
F plasmid is replicated by rolling circle replication
Single strand DNA is transferred to the F- cell through the pilus
Takes about five minutes. Recipient cell now becomes F+
F plasmid
Is what is incorporated into the E. Coli chromosome
Longer cells are in contact, more DNA is transferred
Technique is used to help map E. Coli genome
Hfr strain
High frequency of recombination
Can transfer DNA to recipient strand
What happens of some F plasmid DNA and some chromosomal DNA from the E. Coli strain is transfered?
Will not be Hfr if it does not have the entire strain
Should auxotrophic strain be donor or recipient strain?
Recipient strain
So it initially won’t grow unless they acquire gene from the other strand
Eukaryotic cells and how they are chimeric?
Contain bacterial genes and archaeal genes and genes unique to eukaryotes
Endosymbiosis
Mitochondria and chloroplasts arose from symbiotic relationship of a bacterial cell living inside a larger host cell
Evidence for endosymbiosis
DNA sequences via mitochondrial genes
Are most similar genes of alpha-proteobacteria (Gr-)
Chloroplasts genes are most similar to cyanobacteria
Proteobacteria genomes
~2-4 mbp in size
Human mitochondrial genome
~17,000 bp
Mitochondrial genome
Very few protein encoding genes
Most genes- tRNA, rRNA molecules
Human mitochondria has 13 protein encoding genes
Genes encoding mitochondrial proteins –> most migrated to nucleus
Why is it safe to take antibiotics that target the mitochondrial genome of bacteria?
They impact the mitochondrion ribosomes but they only have 13 protein encoding genes so therefore it is safe to take
Where do eukaryotic cells get their central dogma processes and their metabolic genes/membranes?
Central dogma processes come from archaeal cells
Metabolic genes/membranes come from bacterial cells
Serial endosymbiotic hypothesis of evolution of eukaryotic cell
Eukaryotic cells rose from a nucleus bearing line of archaea. This would explain the central dogma of cells have the archaea origin
Organelles via symbiosis. Genes were transferred to the nucleus
Issues with the serial endosymbiotic hypothesis of evolution?
Membrane lipids
Symbiogenesis hypothesis
Eukaryotic cells arose from a symbiotic relationship of a bacterial cell (H2 producing) and an archaeal cell (H2 consuming)
Bacterial cells is precursor of mitochondrial
Nucleus envolved after genes for membrane synthesis were transferred from bacterial genome to the archaeal genome
Nature paper
Culture independent studies in artic ocean
Found new group of organisms called the lokiarchaeota
Lokiarchaeota
Noticed within these organisms there was 36 proteins that formed a single phylogenetic group with eukaryote
ESP
Eukaryotic signature proteins
Could potentially be an ancestor of eukaryotes (archaeal ancestor of eukaryotes)
Secondary endosymbiosis
Photosynthetic eukaryotes which diverged from green and red algae
Eukaryotic cell incorporated algae to acquire photosynthetic processes
Dinoflagellates
Engulfed red algae to get photosynthetic properties
Euglema
Green algae with ancestors of chloroplasts
Protists
Very diverse group
Single cell microbes
photosynthetic, non photosynthetic
Streamwater
Contains microbes
Eukaryotic microbes
Example is giardia
Giardia
Intestinal pathogen
Not treatable with antibiotics
Contains 2 nuclei that lacks mitochondria and chloroplasts
Produces cysts that are resistant to chlorination
Typamosomes
African sleeping sickness
transmitted by a fly which goes into the bloodstream and can spread to the CNS
Euglena
Broad class of protists
Photosynthetic ones and no photosynthetic (chemoorganotrophs–> get energy by ingesting bacteria) ones
Paramecium
2 nuclei: macro and micro-nuclei
Genome size is > 40,000 genes
Relationships of paramecium
Can be hosts of endosymbiotic bacteria, archaea and eukaryotes
Many different types of symbiotic relationships with other protists
Dinoflagellates
Acquired chloroplasts–secondary endosymbiosis of red algae
causes red tides–occurs in warm polluted waters–toxic species produce a neurotoxin that can kill fish and other organisms in the area
What disease has killed more people than other disease?
Malaria
What causes malaria?
Caused by an organism called plasmodium which is a parasite
Not treatable with antibiotics
There are four types that cause malaria
Has a very complex life cycle
Is transmitted by female anopheles mosquitoes
Life cycle of plasmodium
- Human is bit
- Releases sporozoites into the body that are removed from blood by liver
- Become bigger and form a structure called schizont which segment into smaller cells (merozoites)
- Merozoites leave liver and infect RBC’s
Within RBC’s they replicate. Get fever, chills, weaker at this point - RBC’s undergo meiosis to produce gametocytes. At this point mosquito can take up gametocytes
- Gametes mature there. Fertilization of gametes in mosquitoes. Will develop sporozoites and lifecycle continues
Prevention for malaria
To have universal access to treatments and preventions even as the amount of cases reduces. Make sure all at risk populations have access to preventions and treatments
All countries must be able to upgrade their surveillance of cases. This way the cases can be tracked and interrupt the transmission
Investigating and clearing cases
Vaccine prevention of malaria
Not a one size fits all because of antigenic variation that is great
Life cycle also is complex and makes the vaccine development hard
Disease also does not affect first world countries
There is a new malaria vaccine that has shown being partially effective with a 30% reduction in hospitalizations
Diatoms
Cool looking
cell walls contain silica with proteins and polysaccharides
Yeast
would be a eukaryotic fungi (chemoorganotrophs)
Fungi
Have important symbiotic synthesis with plants
Help plants to acquire nutrients, minerals from the soil
Mineral cycling/nutrient cycling because of their role in decomposition of plants and animals
Can study cancer by looking at their cell division (they don’t get cancer but understanding how cell division works can help with understanding what goes wrong in cancer when you compare cancer to their cell cycle)
How to make bread without yeast?
Flour and water, leave it on counter
Yeast and bacteria from the air
Phylum
Next after domain
Environmental analysis suggests greater than 80 phyla bacteria
Therefore huge amount of diversity
Proteobacteria
Largest phyla in bacteria domain
Well characterized species
Metabolically diverse
Gr - cell wall
Disease causing
What criteria needed for differentiation of bacteria phyla?
Cell wall composition
Genetics
Habitat
Metabolism
Etc…
Rickettsia
Spread by incests
Causes Rocky Mountain spotted fever
Replicates in host cell nucleus
Intracellular parasite
What causes what looks like tree knots?
Bacterial infection
Tumors in the trees are caused by agro bacterium tumefaciens
Agro bacterium tumefaciens
Infects plants
Causes tumors
Infects galls
Has Ti plasmid which is required to cause these infections
DNA is transferred from bacterium to plant
How is the Ti plasmid useful?
Has been notified by researchers so plant species become GMOs
Take out tumor DNA and put in desirable DNA
Creates notified crops
Enteric bacteria
Facultative anaerobes
Oxidase negative
Catalase positive
Different phyla have bacteria with gr + cell walls
Bacillus thuringiensis (Bt)
Is pathogenic to incests
Produces toxin that kills incests
Toxin is called Bt
Bt corn
Transgenic corn that produces toxin to kill incests therefore corn is an insecticide
Negatives of Bt corn
Bt gene can be transferred to other plants
Could kill harmless incests
Ecological impact is not very well understood
Actinomyces
Filamentous bacilli
Common in soils
Streptomyces
Another soil bacterium
Produces antibiotics
Synthesis requires large # of genes
Very large genomes > 8 mbp
Bactroides
Intestinal tract
Obligate anaerobes are present in significant numbers
Large number of genes - carbohydrate metabolism
Chlamydia
Obligate intracellular parasites
Life cycle - 2 forms:
Elementary body: resistant to dry, is used for dispersal
Reticulate body: vegetative form. Divided by binary fission
Bacterial species
Depends on genetics
Membranes of a species:
genetically and phenotypically cohesive, monophylogenetic
Should share common recent ancestor to the exclusion of other species
Pan genome has lots because of horizontal gene transfer
Traits most important
genome/genomic similarity
DNA hybridization
label DNA from one species:
shear it into small pieces
heat it to denature DNA
Second isolate (species/strain):
Denature and shear the DNA
Mix denatured DNA from species 1 and 2
Allow it to cool do DNA strands reanneal
Calculate the percent of the probe hybridized to a control
What do the DNA hybridization values mean?
If the hybridization value is less than 70% then they are separate species
Greater than 70% = same species
Analysis for DNA sequences to figure out if they are related
Analysis of 16S (ribosomal RNA gene) sequences
Same species have 97% identical species
Core genome
Shared by all organisms within the same species
Pan genome
is much larger
Total gene #’s and all strains
So large from horizontal gene transfer
Allows for the acquiring of new genes. Also constant deletion of genes from genome as well if the genes aren’t being used
Why do core genomes not get lost?
Not core since those are proteins with key functions
Most would be essential
What organism do we know the most about?
E. Coli
E. Coli k-12
Common lab strain
~4.6mpb in size and 4,288 genes
One of the first genome to be sequenced
How identical are E. coli K-12 to E. coli 0157:H7
Same species but genetic variation, horizontal gene transfer
E. coli 0157:H7
Can infect hamburger
Best way to characterize microbial community?
Do rRNA gene analysis
Species richness
total number of different species
microbial population
group of microorganism of the same species that reside in the same place at the same time
microbial community
populations of microbial species coexisting in a specific area at the same time
species abdundance
proportion of each species in a community
factors that impact species richness/abundance
nutrients
conditions (O2, temp.)
can also change rapidly
guilds
microbial populations that exploit the same resources in similar ways
Communities of microbes
photic zone: oxygenic phototrophs
oxic zone: aerobes and facultative aerobes
anoxic sediments
Niche
habitat shared by a guild that supplies resources, conditions, that cells require to grow
Biogeochemical cycling
C, N, S, Fe
Resources may be intermittently available
Feast/famine situation for microbes in environment
Some microbes use storage polymers when nutrients are limiting
Phosphates —> polyphosphates
Competition for nutrients
Can be intense
Polyphosphates and sulfur stored in some cells because of this
syntrophy
When microbial species work together to carry out transformation that they could not accomplish individually
Complementary metabolisms
Between different species
One species provides something the other is lacking
ej. ammonia oxidizing microbe reduces nitrate and nitrite. Nitrites are substrates for nitrite oxidizing microbes. Therefore they are often found together
Study of microbes uses:
Culture independent techniques
Culture-dependent techniques
Isolate ~1% of all microbes present
Requirements for microbial growth
Some cases it is unknown
May be dependent on other microbes for growth (big issue in terms of not being able to isolate all the species
Culture independent analysis
Most common way is to isolate DNA from a sample. Want to make sure method for isolating DNA would lyse all cells to get all DNA
Kits available to get bacteria from soil, water, and other sample sites
Pace approach
Use PCR to amplify the 16S ribosomal RNA gene
