Chapter 9.1-9.5

- fertility factor plasmid that contains some chromosomal (host) DNA

F-prime Plasmid

how can pathogen evolve

by losing cellular functions that are supplied by host cell ultimately causing pathogen to be completely dependent on host

in generalized recombination, the enzyme ---- is used to -----

enzyme RecA to find/align homologous stretches of DNA sequences in 2 different DNA molecules

phage preparation can move any gene in bacterial genome to another bacterium

generalized transduction

o Horizontal gene transfers produce most of

genetic variation pathogens while persisting a host

classification of microbes is based on --

hierarchy of ranks (phylym, class, order, and family)

explain how microbe is identified and describe relative advantages and limitations of a dichotomous key as compared with a probabilistic indicator

identifying a microbe by sequencing part or all of its genome dichotomous key- genetic base testing by following a key either answering yes/no questions to narrow species; disadvantage because it is time consuming Probabilistic Indicator- means of quickly identifying microbes in clinical setting based on battery of biochemical tests performed simultaneously on isolated strain; advantage: inherent redundancy

advantage of probalisitic indicator

inherent redundancy

simple transposable element consisting of a transposase gene flanked by short, inverted-repeat sequences that are target of transposase

insertion sequence

based on DNA relatedness

phylogeny

specific plasmid that contains genes needed for pilus formation and DNA export

Fertility Factor (F Factor)

recombination between 2 DNA molecules that share long stretches of DNA sequences

Generalized Recombination (homologous recombination)-

- Describe how gene mobility and DNA recombination lead to emergence of new pathogens

Genes can be moved through horizontal gene transfer through transformation, transduction, and conjugation. These processes generate new combos and pathogens and virulent strains of viruses and bacteria

means of quickly identifying microbes in clinical setting based on battery of biochemical tests performed simultaneously on an isolated strain; top scoring species is then taken as most probably identification

probabilistic indicator

integrated phage genome

prophage

when drug resistant bacteria are isolated from a hospital patient, they may make smaller colonies than the original strain. the reason is ---

random mutation that conferred resistance also conferred deleterious effects on growth

enzyme mediated process by which 2 DNA molecules exchange sections of DNA by cutting and splicing their helix backbones

recombination

loss of traits in absence of selection pressure

reductive evolution

bacterial cell capable of high-frequency recombination caused by presence of chromosomally integrated F factor

Hfr cells

explain how genetic info moves between bacteria by processes of transformation, phage mediated transduction and conjugation

Transformation- recipient bacterium takes up extracellular donor DNA Transduction- donor DNA packaged in bacteriophage infects recipient bacterium Conjugation- donor bacterium transfers DNA to recipient by mating

transposable DNA element that contains genes in addition to those required for transposition; exist in all life forms and can move both within and between chromosomes; cannot replicate outside larger DNA molecule

Transposable Elements/Transposons

a process of DNA transfer into a recipient cell that requires bacteriophage packaging is called

transduction

transfer of host genes between bacterial cells via bacteriophage

transduction

process of moving a transposable element from one DNA region to another

transposition

how to define species

using phylogeny (ribsomal/transcriptional genes) and ecology (cell shape/common habitat)

diagnostic DNA sequencing method that types multiple genetic loci from patient-isolated bacterial cultures in order to identify strain variability

- Multilocus Sequence Typing

how to identify a microbe

- identify isolate to sequence part or all of genome

If F factor is integrated in chromosome, what occurs

1. F factor plasmid integrates into host chromosome 2. cell becomes Hfr capable of transferring genes 3. F factor can be excised, re-forming plasmid 4. F-factor plasmid can include host DNA 5. plasmid carrying host DNA is called F_prime factor

steps of generalized transduction

1. P22 phage DNA infects host ell makes subunits for more phage 2. DNA is packaged into capsid heads; some package host DNA by mistake 3. New phage assembly is completed 4. cell lyses; phage released 5. transducing phage particle injects host DNA into new cell where it may recombine into chromosome

steps of transposition

1. simplest insertion sequence contains gene for transposase and two recognition sites consisting of inverted repeats 2. Transposase binds to elements inverted repeats and makes staggered cut in target sequence 3. Transposon is moved from its original site into target site; element attaches to protruding ends of staggered cut 4. Every time transposable element "jumps" a new duplication forms in target DNA

Why is recombination advantageous to microbe?

1. evolved first as DNA repair useful to fix mutations/restart replication forks 2. damaged chromosomes use DNA to donate others of same species to repair damaged genes 3. self improvement program to obtain genes from other organisms that might enhance competitive fitness of cell

steps of specialized transduction

1. phage DNA integrates into Host 2. copies of phage DNA include adjacent host DNA (gene D) 3. lysis releases progeny phage whose genome includes gene D 4. phage including gene D infects recipient cell 5. phage genome integrate with host genome including gene D from donor cell

steps of conjugation

1. sex pilus from F+ plasmid donor attaches to receptors on recipient cell 2. contraction of pilus draws 2 cells together and forms protein bridge 3. F factor is nicked at oriT and the 5' end begins transfer through bridge 4. strand remaining in the donor is replicated 5. once in recipient, transferred strand circularizes and replicates 6. recipient has been converted to a donor

all of following processes require a step of DNA recombination to integrate the incoming DNA into host chromosome except -- a. transfer of multidrug resistance plasmid b. generalized transduction c. specialized transduction d. transposition of a mobile genetic element

A

which statement does not describe an example of degenerative evolution? a. treponema pallidum- causative agent of syphilis lost many of the genes encoding enzymes of amino acid biosynthesis b. t. pallidum has evolved virulence genes that enable it to take advantage of host cells c. wolbachia bacteria that live within host insect cells lack genes for biosythesis of vitamins d. chlyamydia bacteria are obligate intracellular pathogens that fail to synthesize a peptidoglycan cell wall

B

what describes evidence of highly divergent or distantly related organism? a. genomes of 2 organisms show greater than 70% DNA hybridization b. between 2 genomes, gene sequences that are transcribed to form 16S rRNA show greater than 97% similarity c. orthologous genes of 2 genomes share greater than 95% of same sequence d. 2 genomes show very different proportions of GC vs. AT content

D

Explain how fitness of trait depends on environment and how environment dependent fitness leads to evolution of antibiotic resistance in pathogens

Different environments lead to selection for different traits "fittest" for that particular enzyme. The traits that survive the longest will eventually evolve to occur in descendants. Bacteria have mutation allowing them to survive to live on to reproduce passing onto offspring=fully resistant generation

- How did multidrug resistant come about?

accumulation of signal molecule (ppGpp) that turns on global regulator which enables cell to survive in presence of antibiotics, but slows growth rate due to demands of stress response

suppose pathogenic bacterium acquires a plasmid expressing an enzyme that modifies the target of an antibiotic. What may happen when antibiotic disappears

bacteria containing resistance plasmid will decline, because replicating plasmid costs energy

bacterial viruses composed of nucleic acid enclosed within a symmetrical protein structure called capsid

bacteriophages

bacterium that do what have better chance of survival in nature than cells unable to make distinction

bacterium that can digest invading phage DNA while protecting its own chromosomes

how is microbial species defined

based on sequence similarity of vertically transmitted genes and by principle that members of different species do not normally interbreed with each other

analysis of DNA that compares thousands of sequences through computer algorithms

bioinformatics

explain how bioinformatic analysis helps reveal pathogenesis and physiology of an emerging pathogen

bioinformatics used to interrogate DNA sequences and predict traits of hidden microbiota

which stament describes an example of bioinformatics? a. streptococcus pneumoniae was cultured on various agar media containing different combos of nutrients in order to analyze metabolism b. S. pneumoniae was cultured w/bacteriophage in order to transfer genes between bacteria c. s. pneumoniae isolates were selected for genome analysis which revealed which gene functions were shared and which genes were distinct to different species d. novel isolates of s. pneumoniae were constructed by genetic engineering

c

pathogen identification in a clinical lab is most commonly based on ---

combo of DNA based tests and phenotypic traits

- more complex organization that can carry variety of genes including antibiotic resistance genes

composite transposons

DNA transfer process mediated by transferable plasmid that requires cell-cell contact and formation of protein complex between mating cells

conjugation

- tool for identifying organisms, in which a series of yes/no decisions successively narrows down possible categories of species

dichotomous key

based on shared traits and ecological niche

ecology

organism that lives as a symbiont inside another organism

endosymbiont (ex. wolbachia bacteria)

- Natural selection for the fittest depends entirely on the

envirionment in which selection occurs

- Knowledge of microbes can be used to

interrogate these DNA sequences and predict traits of hidden microbiota

risks involved with indiscriminately accepting transferred DNA

involves bacteriophages whose replication will target cells and unrestricted incorporation of foreign DNA can drain cell

describe how the protection system (restriction and modification) works within bacterium

involves protective methylation of self DNA and enzymatic cleavage of foreign DNA; restrictive endonucleases recognize short DNA sequences and cleave invading DNA

- favors traits that increase survival and reproduction; responds to environmental factors (nutrient availability, temperature, antibiotic presence)

natural selection

critera for working definition of microbial species

o DNA hybridization is 70% or greater than considered species o Small subunit rRNA gene sequence similarity is 97% or greater than o Average nucleotide identity of orthologs is 95% or greater than

How do bacteria protect their own DNA from endonucleases that cleave invading DNA?

o DNA modification enzymes attach methyl groups to host DNA sequences o Methylation makes sequence invisible to cognate restriction enzyme

Describe evolution of endosymbiosis between host cell and an internalized partner organism

pathogens evolve specific traits that enhance ability to colonize host. Eventually pathogen will completely depend on host by losing cellular function

if new DNA is in form of plasmid capable of autonomous replication, plasmid will coexist in cell ---- from host chromosome

separate

recombination between DNA molecules that do not share long regions of homology but do contain short regions

site specific recombination

phage can only move a limited number of bacterial genes

specialized transduction

describe how we define distinct species of bacteria and explain why definition of species is problematic

species- originally defined as members of different species that do not normally interbreed with each other Bacteria and archaea reproduce asexually, so interbreeding is not a basis for classification

disadvantage of dichotomous key

takes more time because of series of steps

description of distinct life forms & their organization into categories; fundamental basis of modern taxonomy is DNA sequence similarity including classificaiton, nomenclature, and identification

taxonomy

reason bacteria make restriction endonuclease is ---

to prevent replication of an invading bacteriophage