Gen 713 Microbial Evolution Midterm
In other cases, when the imported genes remain neutral and there is no obvious benefit associated with their retention, the genes are likely to be __________
lost over time.
explain the 'you are what you eat' gene transfer ratchet in terms of HGT in eukaryotes
many protists (eukaryotes) acquire genes through phagotrophy.
the universal genetic code consists of _____ of the possible 64 nucleotide triplets translating _____ amino acids and the _____ remianing codons (_______, _______, _______) are ______ codons.
61 20 3 UAA, UAG, UGA stop
what 2 other processes influence species formation in microbes?
HGT/LGT gene loss
describe ecotype d model
Homologous recombination between ecotypes can slow the elimination of genetic diversity
horizontal gene transfer is defined as....
Transfer of genetic material between two organisms that do not share a direct ancestor-descendant relationship
actinomycetes
gram + rich GC content form branching patterns called mycelia live in soil -streptomyces is actinomyces
genes that are successfully integrated into a recipient are often expressed at ________ and encode functions at the periphery of ________.
low levels metabolism
•Detection of ancient DNA in conserved specimens that are estimated to be several million years old •In _______ and _______, ~1 μg extracellular DNA can be recovered per g material •In ___________________, ~ 0.03 to 88 μg dissolved DNA can be found per liter
soil and sediments fresh and marine water
disseminated definition
spread throughout
diff between strain vs speacies
strains are variants of a single species
what does robust mean?
strong and healthy
what does endosymbiotic mean?
symbiosis in which one of the symbiotic organisms lives inside the other.
the earliest proteins did not start with.....
the modern set of 20 amino acids
species are ___________ __________ that exist over time
metapopulation lineages
non-canonical amino acids
•Selenocysteine(21st amino acid) -found in all 3 domains of life •Pyrrolysine(22nd amino acid) -found only in some archaea
operational taxonomic units (OTUs) method
•defined as the number of distinct 16S rRNA sequences at a certain cut-off level of sequence diversity •But 16S rRNA possesses insufficient genetic resolution for the reliable binning of microbes into species
But there was no way to decide the order of branching -whether the first divergence in the universal tree separated:
(i) eubacteria from a line that was to produce archaebacteria and eukaryotes, or (ii) a protoeukaryotic lineage from a fully prokaryotic (eubacterial and archaebacterial) clade, or (iii) the (the third and least popular possibility) archaebacteria from eukaryotes and eubacteria.
what is transformation
the uptake of exogenous DNA from the environment.
what is mode?
the way, manner or pattern of evolution; mutational mechanisms and forces driving changes in gene and genome structure
why can most uncultured microbes not be assigned to a classical species? what happens in terms of assignment to these microbes?
- because we dont know their phenotype - Uncultured microbes can be assigned a provisional 'Candidatus' designation if their 16S rRNA sequences are sufficiently different from those of recognized species
the translational machinery consists of.....
- ribosome •Amino acids •tRNAsfor the 20 amino acids •mRNAs •18-20 cognate aminoacyl-tRNAsynthetases(aaRS) •at least 7-8 translation factors
The underlying assumption is that some contemporary processes and molecules had to appear ________________ and that the evolution of the information processing system involved what?
-before others -interactions between separately evolving components.
in prokaryotes the recombination processes.... -can cross ________ boundaries -entail the movements of __________ of chromosomes rather than ________ chromosomes - does not result in __________ evolution
-taxonomic -fragments, whole - tree-like
______% of internalized DNA fragments are successfully recombined in Acinetobacter baylyi, whereas up to 25-_____% of the internalized DNA fragments are recombined in Bacillus subtilis and Streptococcus pneumoniae
0.1 50
4 Stages through which DNA must go on its journey from donor to recipient bacteria
1. DNA becomes available 2. Development of competence &/or binding of DNA to the surface 3. stable uptake 4. integration into the chromosome
4 methods to define microbial species
1. DNA-DNA hybridization 2. multilocus sequence analysis (MLSA) 3. average nucleotide identity (ANI) 4. operational taxonomic units (OTUs)
what was the 1st main finding of the woesian tree of life?
1. Eukaryotic host not related to any specific prokaryotic lineage •Unexpected because endosymbiont hypothesis predicts endosymbiotic host arising within the bacteria •(Nuclear-cytoplasmic) ribosome of LUCA was a primitive ribosome. Same with other informational components of the ancestral cell (progenote) •Prevalent view in the 80's and early 90's: - The prokaryote/eukaryote dichotomy remained but as a vertical split, separating living things into two camps from the very beginning rather than marking a more recent but crucial transition in the grade of cellular organization. - Refinement of cellular functions occurred separately in the primary lines of descent, after they have diverged from the common ancestral progenote
movement of antibiotic resistance genes (3 ways)
1. Physical forces (wind, running water, desert dust, storms, wind) 2. humans -Antibiotic resistance genes have been transmitted to the most isolated human populations, where they exist even in the absence of an obvious selection pressure. 3. animals •Proximity to human activity and dense human settlements •Migratory animals
what are the 3 phases of the evolution of the information transfer system of modern cells?
1. Pre-Darwinian Evolution: No replication, nothing for natural selection to work on 2. Progressive-Darwinian Evolution: Separately evolving components interacting with each other; Fixation of mutations that improves info transfer 3. Post-progressive-Darwinian Evolution: Fixation of mutations conferring fitness in specific environments
why are hidden paralogs an issue?
they can mislead tree topolgy
mechanisms of antibiotic resistance in gram neg bacteria (40
1. impermeable barrier (outer membrane) 2. efflux pumps 3. resistance mutation 4. drug inactivation
what are the 3 principal scenarios of code origin and evolution?
1. stereochemical hypothesis 2. coevolution (metabolic) hypothesis 3. error-minimization hypothesis
Co-evolution of the genetic code and the translation system (3 things) IMPORTANT
1.Amino acids are postulated to have been recognized by unique pockets in the tertiary structure of the proto-tRNAs. 2.The grouping of codons for related amino acids underlying error minimization naturally follows from code expansion through duplication of the proto-tRNAs. 3.Once the specificity determinants migrated from the proto-tRNAsto the aaRSs, the amino acid-binding pockets in the tRNAsdeteriorated such that modern tRNAsshow no detectable affinity to the cognate amino acids.
Four hypotheses to explain present-day distribution of microbes:
1.Microbes are randomly distributed over space. 2.Baas-Beckinghypothesis: "Everything is everywhere, but the environment selects." •Reflects the influence of contemporary environmental variation •"everything is everywhere": Enormous dispersal capabilities such that they erase the effects of past evolutionary and ecological events •"but the environemtn selects": Different contemporary environments maintain distinct microbial assemblages. 3. All spatial variation is due to the lingering effects of historical events. 4. Microbial distribution reflect the influences of both past events and contemporary environmental conditions?
first method of homology-based recombination
1.Recombination that occurs between two circular molecules or between a circular molecule and the bacterial chromosome leads to additive integration. •This process is based on single crossovers at short regions with high DNA-sequence similarity and leads to the fusion of plasmids or other circularized DNA molecules, or the integration of circular DNA molecules into the bacterial chromosome
3 things we know about the genetic code
1.The code is nearly universal: Departures from code universality in extant organisms are minor and of secondary origin. 2.The code is non-randomly organized and is highly robust to errors, although it is far from being globally optimal. 3.Evolution of the code involved expansion from a limited set of primordial amino acids toward the modern canonical set.
•Modifications to the code belong to three major categories:
1.reassignment of codons within the canonical set of 21, including the stop signal 2.loss (unassignment) of codons 3.incorporation of new amino acids
•Any theory of why the standard genetic code is the way it is and how it came to be must address three key facts:
1.the code's REGULARITY as expressed in non-random amino acid assignments 2.its OPTIMALITY as expressed in its robustness against errors in translation from code sequences to proteins and in replication of genetic material 3.its near UNIVERSALITY across extant biological systems.
Microbial taxonomy: ______ used as a standard to classify bacteria and archaea
16S rRNA
what was the second main finding of the woesian tree of life?
2. Two deeply divergent prokaryotic groups (EUBACTERIA, ARCHAEBACTERIA, eukaryotes) - ... the three urkingdomsto be equidistant from one another." - note, archaebacteria is known called archae •Includes: Methanogens, halophiles, thermophiles, psychrophiles, and other extremophilicorganisms
second method of homology-based recombination
2.Recombination that occurs between linear DNA and chromosomal DNA molecules can also lead to the additive integration of DNA. •In this process, once recombination has been initiated in a single region of high DNA similarity, the strand exchange extends into regions of little or no nucleotide-sequence similarity, resulting in substitution of DNA sequences or often the integration of additional DNA sequences. •Recombination processes that extend into areas with little similarity have been named homology-facilitated illegitimate recombination (HFIR)http://
recombination occurs between chromosomal DNA that is less than _____% divergent
25
•LUCA, which lived over 3 billion years ago, was not the first cell to appear on our planet. •Comparative genomics has demonstrated the existence of ____ RNA molecules and ____ ribosomal proteins common to all living organisms and also therefore to LUCA. •Given their complexity, these molecules could only have appeared after a long period of _________. •LUCA must therefore have shared the planet with many other organisms resulting from this same time span. •However, its contemporaries left no descendants, which is not to say that they did not hand down certain genes to us, just as the Denisovansand Neanderthals did with ourHomo sapiensancestors.
3 34 evolution
third method of homology-based recombination
3. Additive integration of DNA, based on two flanking (one on each side) regions of high DNA similarity to initiate the recombination process - so basically the foreign DNA has segments at beginning and end that match chromosomal DNA that only has those 2 segments, so the entire foreign DNA is added (additive integration) foreign: x-o-o-o-w chromosomal: x-w
streptomyces produce more than_____ % of all known antibiotics
50
Prochlorococcus pan-genome has been estimated to contain approximately _______ genes. Individual genomes encode only about _______ genes each
58,000 2,000
in terms of species definitions in micro, reciprocal, pairwise DNA re-association values are ≥____% in DNA-DNA hybridization experiments under standardized conditions and their ΔTm(melting temperature) is ≤___°C. All strains within a species must possess a certain degree of __________ consistency, and species descriptions should be based on more than one type _____
70 5 phenotypic strain
gram neg characteristics
thick impermeable cell membrane have outer cell membrane - thin peptidoglycan layer
what is hormesis?
A dose-dependent response phenomenon shown by bioactive compounds and drugs, such that they have contrasting activities at low (subinhibitory) and high (inhibitory) concentrations.
holobiont
A multicellular or unicellular host and its collective symbionts
abiotic vs biotic
Abiotic: non-living Biotic: living
describe ecotype model a
All related inhabitants of a unique ecological niche are thought to belong to a single, stable ecotype, within which overgrowth by fitter variants (periodic selection) repeatedly eliminates the genetic diversity that accumulates over time * Periodic selection places limits on the genetic diversity within an ecotype, but does not prevent the divergence of other, non-competing ecotypes in distinct niches, nor does it limit their diversity
replacement HGT: •_____________ replacement through homologous recombination between closely related organisms •Creates novel combinations of _______
Orthologous alleles
HGT acquired genes: Selective advantage/ positive effect to recipient will lead to....
Bacteria can potentially spread rapidly within the population
HGT acquired genes: Deleterious/negative effect to recipient will lead to....
Bacteria will be lost in the population over time
____________ in the gut of Japanese people can break down polysaccharides from the cell walls of seaweeds that are commonly present in the Japanese diet. where did these genes encoding seaweed polysaccharide breakdown come from? This HGT has enabled Japanese people to use carbohydrates from algal cell walls as a nutrient source, whereas other populations cannot.
Bacteroides - genes were transferred from bacteria of marine algae to the gut bacteria.
what is Darwin's idea of descent with modification
Basically, by looking at the pattern of modifications (novel traits) in present-day organisms, we can figure out—or at least, make hypotheses about—their path of descent from a common ancestor.
DNA-DNA hybridization method
DNA is heated to denaturation temperature to form single strands and then when cooled, double helices will re-form (renaturation) at regions of sequence complementarity •the more closely related two species are, the greater will be the number of complementary base pairs in the hybrid DNA •Cut-off value of ≥70% to define a species
•From 1545 to 1548, a mysterious disease killed about 80 percent of the population of Mexico.It was one of the worst epidemics in human history, felling an estimated 5 million to 15 million people, and was known by natives ascocoliztli—a word meaning pestilence. •About three decades later, cocoliztli struck again, wiping out half of the remaining native population between 1576 and 1578
DNA was extracted from the teeth of people who dies in this 16th century epidemic •... to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. •This cemetery is linked, based on historical and archaeological evidence, to the 1545-1550 CE epidemic that affected large parts of Mexico. •Locally, this epidemic was known as 'cocoliztli', the pathogenic cause of which has been debated for more than a century. •Genome-wide data from ten individuals for Salmonella entericasubsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever.
DNA-DNA gybridization
DNA-DNA hybridization generally refers to a molecular biology technique that measures the degree of genetic similarity between pools of DNA sequences. It is usually used to determine the genetic distance between two organisms. This has been used extensively in phylogeny and taxonomy
lineage
a metapopulation that extends through time, occupies an adaptive zone minimally different from that of any other lineage in its range, and evolves separately from all lineages outside its range
what is a methanogen?
a methane-producing bacterium, especially an archaean which reduces carbon dioxide to methane.
The development of the nucleus sequestered genetic material in eukaryotes made gene exchange a more complicated process, although physical association over extended periods of time can facilitate HGT. ________________ as a stable form of physical association often leads to the presence of foreign genes in eukaryotic genomes.
Obligate endosymbiosis
cenancestor aka __________ is similar to modern ________
LUCA bacterium
review of cellular translation:
Each amino acid is attached to the corresponding tRNAby a specialized aminoacyl-tRNAsynthetase(aaRS), in a reaction called aminoacylation. An aminoacyl-tRNAsynthetase(aaRS) recognizes a unique tRNAand charges it with the cognate amino acid. The resulting aminoacyl-tRNA(aa-tRNA) products of the aaRSsread codons by codon-anticodon pairing between mRNA and tRNAon the ribosome.
endosymbiont hypothesis
Endosymbiotic host (eukaryote) arose within the bacteria, lost its cell wall and acquired the ability to engulf other cells
gene duplication
Gene duplication happens when an extra copy of a gene is made in an organism's genome. In some cases, the duplication leads to the gain of a new function, but in other cases, protein function is lost
genetic drift
Genetic drift describes random fluctuations in the numbers of gene variants in a population. Genetic drift takes place when the occurrence of variant forms of a gene, called alleles, increases and decreases by chance over time. Typically, genetic drift occurs in small populations, where infrequently occurring alleles face a greater chance of being lost
describe ecotype e model
LGT (lateral/horizontal gene transfer) can facilitate the continual emergence of new ecotypes, with concomitant (naturally accompanying), continuous extinction of other competing ecotypes
what are orthologs?
Orthologous genes are homologous genes that diverged after evolution gives rise to different species, an event known as speciation. The genes generally maintain a similar function to that of the ancestral gene that they evolved from.
isolation by distance
Pairs of populations close to each other will be more genetically similar to each other than populations farther away from each other, not because of any selective need for those genetic similarities, but just because individual critters, or their seeds, or pollen, or larvae are less likely to travel longer distances.
what are paralogous genes?
Paralogous genes are homologous genes that have diverged within one species. Unlike orthologous genes, a paralogous gene is a new gene that holds a new function. These genes arise during gene duplication where one copy of the gene receives a mutation that gives rise to a new gene with a new function, though the function is often related to the role of the ancestral gene.
alternative scenario of S. Typhi regarding periodic selection
Periodic selection might be so rare that all S. Typhi strains are derived from a single ecotype that has not undergone periodic selection over many millennia.
what was responsible for the transformation of cyanobacterial endosymbionts into modern-day plastids?
Several analyses identified 20-50 genes from chlamydiae, a group of obligate intracellular bacteria, in various photosynthetic eukaryotes. These findings led to the suggestion that cyanobacterial and chlamydial endosymbionts coexisted in an early eukaryotic host cell
describe ecotype model b
Single ecotypes can also encompass multiple clusters of genotypes. -Geographical separation may cause this
define a sepcies
Species are groups of actually or potentially interbreeding individuals, reproductively isolated from other groups but can we use this definition for microbes?
HGT acquired genes: neutral effect to recipient will lead to....
Survival of bacteria will depend on chance
homologous recombination (microbes)
The acquisition of DNA segments from closely related microbes via recombination at flanking (each side of) homologous sequence stretches
why is the Tree of Life a problematic framework in microbial evolution?
The assumption of a universal Tree of Life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. •However, the gene histories for a large majority of a microbe's genes are discordant, which means that the traditional Tree of Life model is very much a problematic framework to study microbial evolution.
what is the strongest available evidence that some form of LUCA actually existed
The conservation of the core of the translation machinery
Ernst Mayr: Biological species concept
The existence of plant and animal species is due to the cohesive evolutionary forces that result from pre-zygotic and post-zygotic barriers between eukaryotic species
mitochondrial eve (second definition)
The first female ancestor shared by all living humans, who was identified by analysis of mitochondrial DNA.
transformation frequency
The number of bacteria carrying the horizontally acquired DNA divided by the total number of bacteria exposed, per given time unit
hybridization
The process of forming a double stranded nucleic acid from joining two complementary strands of DNA (or RNA) - crossing dissimilar individuals
the standard genetic code is not optimal. explain this
The standard genetic code (SGC) is not optimal: Given the overall hyper-astronomical number of possible codes (>1084), billions of variants are more robust than the actual universal code. **** read up more on this in papaer
note on methods to define microbial species :
These cut-off values are not based on any particular theoretical justification, but instead was chosen 20 years ago to match pre-existing species definitions
what is Outgroup rooting in phylogenetics?
We can root any sequence-based tree relating a restricted group of organisms (all animals, say) by determining which point on it is closest to an "outgroup" (plants, for example).
describe ecotype model c
When the population size is small, genetic diversity can persist owing to genetic drift, instead of being eliminated by periodic selection
why did adam and eve never meet?
Y chromosome adam tMRCA lived about 338,000 years gao Mitochondrial Eve tMRCA lived about 180,000 years ago
Microbes that dwell in the guts of Japanese people but not in North Americans have some of the same seaweed-digesting enzymes as the marine bacterium ____________.
Zobellia galactanivorans
ecotype
a genetically distinct geographic variety, population or race within a species, which is genotypically adapted to specific environmental conditions
haplotype
a group of genes within an organism that was inherited together from a single parent
what is a ribosome?
a large complex of at least 3 RNA molecules and 60-80 proteins; the most ancient, universal molecular structure in all cells
what is drug inactivation
a mechanism of antibiotic resistance in gram neg bacteria - Inactivation can occur by covalent modification of the antibiotic, such as that catalysed by acetyltransferases (purple) acting on aminoglycoside antibiotics, or by degradation of the antibiotic, such as that catalysed by β-lactamases (brown) acting on β-lactam antibiotics
cyanobacteria
a phylum of bacteria that obtain their energy through photosynthesis and are the only photosynthetic prokaryotes able to produce oxygen
Influence of HGT to recipient lineage: For a transferred gene to survive in the recipient lineage for long periods of time, the gene usually needs to provide....
a selective advantage either to itself (in the case of a selfish genetic element) or to the recipient.
average nucleotide identity (ANI) method
a similarity index between a given pair of genomes •a cut-off score of >95%indicates that they belong to the same species
what is an outgroup?
a taxonomic unit that branched off in evolution prior to the existence of the common ancestor of all the taxa being studied in an ingroup
ecological niche
a term for the position of a species within an ecosystem, describing both the range of conditions necessary for persistence of the species, and its ecological role in the ecosystem.
Acquisition of DNA through additive integration leads to the acquisition of
additional DNA material from donor DNA
explain the Frozen Accident Theory (Francis Crick)
after the primordial genetic code expanded to incorporate all 20 modern amino acids, any change in the code would result in multiple, simultaneous changes in protein sequences and, consequently, would be lethal, hence the universality of the code. •Attempts to explain the universal nature of the Genetic Code and the fact that it only contains information for twenty amino acids. •Refers to the notion that the standard code might have no special properties but was fixed simply because all extant life forms share a common ancestor, with subsequent changes to the code, mostly, precluded by the deleterious effect of codon reassignment.
The differences between archaebacteria and either eubacteria or eukaryotes were of a sufficiently fundamental nature to indicate that.....
all three primary kingdoms must have begun to diverge during the period of progressive evolution from a progenote.
sequence-independent DNA-uptake
allows translocation of both plasmids and chromosomal DNA across their membrane(s)
Binding interactions between __________ and their _______ or ___________ dictated the structure of the genetic code IMPORTANT
amino acids codons anticodons
province
any geographic area, the biota (life) of which reflects historical events
endosymbiont
any organism that lives within the body or cells of another organism in a mutualistic (formerly called symbiotic) relationship with the host body or cell, often but not always to mutual benefit.
planctomycetes are considered ____________. But what characteristics make that characterization difficult?
bacteria •intracellular compartmentalization •lack of peptidoglycan in their cell walls •a membrane-bound nucleoid analogous to the eukaryotic nucleus •'anammox' planctomycetes have a unique anaerobic, autotrophic metabolism that includes the ability to oxidize ammonium; this process is dependent on a characteristic membrane-bound cell compartment called the anammoxosome, which might be a functional analogue of the eukaryotic mitochondrion. •Uptake of proteins from the external medium through a process that is associated with internal vesicle formation and which thus resembles eukaryotic endocytosis (membrane coat-like proteins)
sequence-specific uptake
based on short (~9-11 bpin length), interspersed (~4-5 kb apart) nucleotide motifs in the bacterial genomes •likely restricts uptake of plasmids and transfer of chromosomal DNA between distantly related genera
why cant we use organismal outgroup for a universal tree?
because all organisms are already included in that tree
why is the importance of biosynthetic pathways for the code evolution almost self-evident? IMPORTANT
because amino acids could not be incorporated into the code unless they were available.
why are quantification of bacterial and archaeal HGT difficult?
because most transfers occur between closely related organisms and are difficult to distinguish owing to the genetic similarity of the host and the recipient genomes.
habitat
environment defined by the suite of abiotic and biotic characteristics
pre-antibiotic era
before the late 1930's •can be considered 'antibiotic naive', in the sense that no industrial production of antibiotics took place. •Determinants of antibiotic resistance existed naturally and were probably subject to horizontal transfer long before the extreme selection pressure that was imposed in the antibiotic era.
These neutral acquisitions, however, can later provide novel combinations of genetic material for selection to act on —in some cases, the transferred material becomes domesticated over time and produces a __________________.
beneficial phenotype
what does dichotomy mean?
branching into two equal parts, separating
where re most antibiotics produced from?
by strains of fungi and bacteria that occur naturally in all environments, including soil
what are gene transfer agents (GTAs)?
carry small random pieces of host genome in capsids for delivery to nearby hosts. GTAs have evolved from prophages that have lost the ability to target their own DNA for packaging. Like prophage, they reside in the host cell genome.
Neisseria meningitidis (cause of......)
cause of epidemic cerebrospinal meningitis •Population structure of which seems to resemble that of the species-less ecotype model •Sequence diversity in these organisms accumulates rapidly over a period of several years, largely owing to homologous recombination •Caused by repeated extinction of genotype clusters (called 'genoclouds') •Rapid, apparently random, successions of genocloudsare attributed to geographic bottlenecks during epidemic spread that amplify the first strain to pass the bottleneck
Yersinia pestis (cause of ________) facts
cause of plague •Flea-born transmission between rodents •pestis a clone of pseudotuberculosis (gastrointestinal pathogen); indistinguishable and would not form distinct species based on current species definition methods •But considered as separate species: independent evolution, distinct ecological niche and mechanism of transmission •pestis population structure resembles the expectations of genetic drift, rather than periodic selection, but ecotypes unknown •Very few SNPS, eight populations but unknown number of ecotypes
Biased gene transfer and highways of HGT: •HGT is more frequent between _______________ species. •The frequency of successful HGTs between pairs of Haloarchaea was shown to ________ exponentially with the phylogenetic distance, •Likely due to the reduced efficiency of _______________ between genetically divergent organisms.
closely related decrease homologous recombination
For natural transformation to occur, cells must first develop a regulated physiological state of ___________
competence
list the mechanisms of HGT
conjugation transformation transduction intracellular or endosymbiotic HGT gene transfer agents (GTAs) cell fusion
accessory genome
contains genes that are present in only one or a few members of the taxon. the non-core genes in a strain's genome
plastid
cytoplasmic bodies within a plant cell
in building a tree, we organize species into nested groups based on shared ________
derived traits (traits different from those of the group's ancestor).
monophyletic
descended from a common evolutionary ancestor or ancestral group, especially one not shared with any other group.
allometry
describes the relationship of one part of a organism to another part; relationship of body size with other traits
Different ecotypes are free to _______ without constraint from one another
diverge
The evolution of the code is thought to be driven by positive selection for .... IMPORTANT
diversification of protein functionality enabled by the incorporation of new amino acids.
The basic molecular machinery of meiotic recombination and sex was present in the ______________
eukaryote common ancestor.
For many multicellular __________, the number of genes in the microbiome (microorganisms in a particular environment) dwarfs the number of genes in the ______________ of the host and provides an important source of genetic diversity.
eukaryotes nuclear genome
Recombination with host genome: homologous recombination depends on what types of segments of DNA? •Results to simple ____________ that preserve the size and functionality of the recombined area •Depending on the system, the incoming DNA must contain regions between _______ bp in length of high similarity to the recipient genome. •These regions will initiate DNA pairing and strand exchange.
extensive segments of high sequence similarity between two DNA molecules. DNA replacements 25-200
population bottleneck
extreme reduction in population size
3 ways of homology-based recombination
fact
Genes that adapt an organism to a particular niche are also transferred between niche boundaries, and such HGTs might help recipients to integrate into a new ecological niche.
fact
Some genes confer antibiotic resistance but are likely to have other primary roles in the environment (e.g., tolerance to toxic compounds of heavy metals)
fact
Woese believed that eukaryote/ prokaryote is not primarily a phylogenetic distinction, although it is generally treated so."
fact
gene tree vs. species tree: not all genes have the same evolutionary history as the other genes in a lineage or even of the organism itself.
fact
in eukaryotes, Meiosis ensures reciprocal recombination among homologous chromosomes and reassortmentof alleles within lineages that recombine within or very near (in the case of hybridization) species boundaries
fact
phylogenetic trees may be built using morphological (body shape), biochemical, behavioral, or molecular features of species or other groups.
fact
taxa and species can be used interchangably
fact
in gene loss, most sequence changes are evntually lost, especially if they reduce __________
fitness -Loss of function during adaptation to a new host-
Internalized DNA will normally persist only transiently in the bacterial cytoplasm owing to the inability of DNA fragments to replicate during bacterial cell division. If the DNA is reassembled as double-stranded DNA in the cytoplasm, restriction enzymes might cause rapid _______________
fragmentation.
give example of biocontrol
fungus-growing ant system, in which ants carry an antibiotic-producing actinomycete(a Pseudonocardia sp.) on their cuticle and use this bacterium specifically for biocontrol of the fungal garden parasite, Escovopsis sp
taxon
group or level of organization into which organisms are classified
what do phylogenetic trees represent?
hypotheses about the evolutionary relationships among a group of organisms.
what is additive HGT
integration of novel genetic material into a genome E.g., >1,000 genes were identified as imports from bacteria into Haloarchaea, including those for carbon assimilation, respiratory chain complexes, membrane transporters and cofactor biosynthesis. The influx of these bacterial genes allowed the haloarchaeal ancestor to move into an aerobic environment.
what is cell fusion?
involves exchange of DNA bi-directionally after cell contact and bridge formation between two cells.
SNPs
is a DNA sequence variation occurring when a single nucleotide adenine (A), thymine (T), cytosine (C), or guanine (G]) in the genome (or other shared sequence) differs between members of a species or paired chromosomes in an individual. creates alleles
population
is all of the individuals of the same species within an ecological community.
what are efflux pumps?
mechanism of antibiotic resistance in gram neg bacteria - These pumps secrete antibiotics from the cell. Some transporters, such as those of the resistance-nodulation-cell division family (pink), can pump antibiotics directly outside the cell, whereas others, such as those of the major facilitator superfamily (red), secrete them into the periplasm.
from Woese tree of life, of the 3 primary kingdoms as domains, ___________ and __________ are archaezoans thought to have diverged from the rest of the eukaryotic nuclear lineage before the aquisition of mitochondria or plastids through endosymbiosis
microsporidia giardia
Early cellular evolution differed in both _____ and ______ from the contemporary process.
mode tempo
HGT contributes to the rapid creation of biological novelty that otherwise might have taken millions of years to occur (through _______ alone)
mutation
when was LUCA named? how old is LUCA thought to be?
named about 20 years ago thought to be more than 3 billion years old
transformation: - has stable uptake, integration and functional expression of extracellular DNA that can occur under _________________ conditions - the only mechanism that can potentially explain how bacteria acquire DNA from ____________ beyond the host range of mobile genetic elements or bacteriophages
natural bacterial growth foreign species
Darwin's theory of descent with modification operates with just two mechanisms acting over vast spans of geological time :
natural variation (or heritable variation) natural selection
many of the genes that have been identified as transferred through comparative genomics between close relatives have ______________ effects in the recipient
neutral or nearly neutral
gram positive membrane
no outer cell membrane thick peptidoglycan layer
Uptake of DNA into the bacterial cytoplasm: •Upon exposure to competent bacteria, the extracellular DNA binds _______________ to sites present on the cell surface. •________ is converted to ________ during translocation across the inner membrane •Some competent bacterial species (e.g., Neisseria gonorrhoeaeand Haemophilusinfluenzae) are _________ in the DNA they translocate across the membrane, whereas most other species take up DNA independently of its sequence
non-covalently dsDNA ssDNA selective
illegitimate recombination
occurs in regions where no large-scale sequence similarity is apparent, e.g. translocations between different chromosomes or deletions that remove several genes along a chromosome •through double-stranded breaks and end-joining
what is introgression?
occurs when a hybridization event occurs between two diverging species (orange and blue populations). Backcrosses with one of the parent populations (orange) can lead to only a small piece of the divergent genome (blue) remaining in the recipient.
what is intracellular or endosymbiotic HGT?
occurs when genetic material from an endosymbiont or organelle (such as a chloroplast or mitochondrion) is incorporated into the host genome (eukaryotes).
homologous chromosomes
pairs (one from each parent) that are similar in length, gene position, and centromere location. The position of the genes on each homologous chromosome is the same, however, the genes may contain different alleles
Each individual genome thus represents a sample from the ___________. The ____________ also represents the set of genes that is potentially available via HGT to any member of the group.
pan-genome.
Genetic diversity within an ecotype is limited by a force of ______________
periodic selection
multilocus sequence analysis (MLSA) method
phylogenetic analyses of multiple (typically 6-8) single copy, protein-coding core genes •form discontinuous sequence clusters
what are some sources of natural variation?
point mutations chromosome replication errors vertical inheritance (parent to offspring)
explain shift from primordial stereochemical code to modern translation
primordial stereochemical code is thought to have been simply amino acid- proto tRNA recognition. then there was code expansion from duplication of the proto-tRNAs which caused grouping of codons for related amino acids underkying error minimization (why the codon chart is uniform and similar codons code for similar aa) Once the specificity determinants migrated from the proto-tRNAs to the aaRSs, the amino acid-binding pockets in the tRNAs deteriorated such that modern tRNAs show no detectable affinity to the cognate amino acids. *** pic at end of 1/30 pp
The _________ of natural variation is uniform across all life, the ________&_________ underlying it are not.
principle processes and mechanisms
progenote/primitive means....
progenote is another name for LUCA primitive means early stage of evolution
point mutations and replication errors are common to both ______ and ______
prokaryotes eukaryotes
The uptake of DNA by competent bacteria occurs ________ in vitro what is the speed in streptococcus pneumoniae and acinetobacter baylyi?
rapidly about 100bp/second in Streptococcus pneumoniae and 60bp/second in Acinetobacter baylyi
what is tempo?
rate of evolution; amount of change relative to a standard
what is conjugation?
requires physical contact between a donor and a recipient cell via a conjugation pilus and single-stranded DNA is transferred from the donor cell to the recipient cell.
Most antibiotic-producing strains carry genes encoding __________ to the antibiotics that they produce
resistance
_____________ mutations modify the target protein, for example by disabling the antibiotic-binding site but leaving the cellular functionality of the protein intact.
resistance
Recombination events resulting in nucleotide changes of only a few bp can be difficult to distinguish from genetic changes arising from _______________, and the mechanism responsible, HGT, is therefore easily overlooked
sequential mutations
metapopulations
sets of connected subpopulations (one or more related populations at any one time) that are maximally inclusive and the limits of which are set by evolutionary cohesive forces (online definition) a group of populations that are separated by space but consist of the same species.
transient
short-lived
what is transduction?
the delivery of genetic material through phage predation owing to the integration of exogenous host genetic material into a phage genome. - bacteriophage enters host and host DNA transferred to phage then phage infects another bacteria and gives it the DNA from first host bacteria
homologous recombination
the exchange of genetic material between two strands of DNA that contain long stretches of similar base sequences
Minimum inhibitory concentration (MIC)
the lowest concentration of an antimicrobial that will inhibit the visible growth of a microorganism after overnight incubation
what is mitochondrial eve?
the matrilineal most recent common ancestor (MRCA) of all currently living humans, i.e., the most recent woman from whom all living humans descend in an unbroken line purely through their mothers
LUCA emerged when all of its components.......
the ribozymes, genetic code, and proteins were functioning in full synchrony.
what does the genetic code define?
the rules of translation from the 4-letter nucleic acid alphabet to the 20-letter alphabet of proteins
pan-genome
the set of all genes present in a taxon. the totality of the genes present in the different strains of a species
core genome
the set of genes present in every member of the taxon.
in prokaryotes, genetic variation can arise via multiple mechanisms such as.....
transformation transduction conjugation gene transfer agents intergons
The persistence of extracellular DNA will determine the bacterial exposure time, and therefore the natural ________________. -Persistence also depends on environmental conditions.
transformation frequency
Rather than reflecting adaptive increases in fitness, a considerable proportion of the genetic diversity between individual strains within a species, including genes introduced by LGT, is ......
transient and lost over time
Evolution of the code is intimately linked to the origin and evolution of the ______________ itself and this is one of the most fundamental and hardest problems in all of biology and the origin of life.
translation apparatus
Mutations inherited via chromosome replication and cell division give rise to___________ over time
tree-like structures
Over geological time that process, which includes chromosome replication errors, generates what?
treelike structures during eukaryote evolution.
HGT/LGT leads to what?
unexpectedly high levels of variation in gene content within individual species •Genomic comparisons between strains of E. coli revealed that 8-21% of the genes within each genome were specific to single strains
homologous recombination: incorporation of DNA from a donor cell into the genome of a recipient cell; ____________ (uni or bidirectional?) and always ___________ of reproduction (cell division)
unidirectional independnt
In the context of a donor and a recipient cell, the genetic variation processes of recombination in prokaryotes are always _________, never _________.
unidirectional reciprocal
The genetic code is nearly ___________, and the arrangement of the codons in the standard codon table is highly ___________.
universal non-random
how does DNA continually enter the environment?
upon release from decomposing cells, disrupted cells or viral particles, or through excretion from living cells
difference between vertical gene transfer and horizontal gene transfer
vertical = transfer of genetic material from parent to offspring horizontal = transfer of genetic material between unrelated individuals
homology-based recombination occurs between DNA molecules of _____________
very similar sequence
The recently proposed _____________ model suggests that weakly protected unicellular or early developmental stages, especially in oviparous species, might constitute potential entry points for foreign genes into multicellular eukaryotes. These foreign genes could then be spread through _______ to germline cells, and thus to offspring.
weak-link mitosis
what are homologs
when common gene sequences in 2 different species is a result of a common genetic ancestor
describe amino acids in prebiotic chemistry
•10 amino acids are consistently produced in prebiotic chemistry experiments and also have been identified in meteorites in the following order of relative abundance: Gly, Ala, Asp, Glu, Val, Ser, Ile, Leu, Pro, Thr •These 10 can be confidently considered old; i.e., they were represented already in the first proteins.
describe the chicken and egg problem in terms of transcription
•A high-fidelity translation system requires a number of functional proteins, but the maintenance of such proteins is impossible without a reliable translation system. •The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system.
ways cells excrete DNA
•Active excretion of DNA •Passive release of DNA from dead bacteria occurring after self-induced lysis, a process that results in broken cell walls and membranes and the subsequent exposure to, and release of, cytoplasmic contents, including DNA, in the environment •Persistence of extracellular DNA in environment varies
explain genetically monomorphic pathogens. what are they evidence against?
•Bacterial pathogens with low synonymous sequence diversity (DSof <0.0002) •low levels of neutral sequence diversity Some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called 'genetically monomorphic bacteria' evidence against ecotype model
describe the stereochemical hypothesis IMPORTANT
•Codon assignments for particular amino acids are determined by a physicochemical affinity that exists between the amino acids and the cognate nucleotide triplets (codons or anticodons) •Thus, under this class of models, the specific structure of the code is not at all accidental but, rather, necessary and, possibly, unique.
where is provotellaceae commonly found?
•Commonly found in the digestive tracts of people who maintain a diet low in animal fats and high in carbohydrates (vegetarians and non-Westerners). •Found in other parts of the microbiome like the genitals and respiratory tract. •Predominant ones found on uncircumcised penises.
facts about the universal code and LUCA
•Comparative-genomic reconstructions of the gene repertoire of LUCA point to a complex translation system including at least 18 of the 20 aaRS, several translation factors, at least 40 ribosomal proteins, and several enzymes involved in rRNAand tRNAmodification; thus, it appears that the core of the translation system was already fully shaped in LUCA. •The canonical code emerged before the LUCA; all life following the LUCA inherited this canonical code nearly ubiquitously.
what is the problem with the gene duplication rooting approach?
•Difficult to align sequences that have diverged a long time ago •Difficult to distinguish orthologsvs. paralogs Orthologs-arose by speciation event Paralogs -arose by duplication event
how can the 3 hypothesis all be correct?
•Error minimization and coevolution are, in generalized form, both potentially compatible with stereochemical origins for some codons because each requires a starting code from sources potentially distinct from its own mechanism. •The three processes are complementary rather than competitive and could have occurred simultaneously, even though they are often posed as alternatives.
microbial species and sequence clusters (* dont really get this)
•In some microbes, delimited sequence clusters correlate well with classical species definitions for species. •The neutral genetic diversity within these datasets indicates that many classical species contain multiple populations and may well correspond to metapopulation lineages. •Not all isolates fall into a sharply circumscribed genotype cluster because of frequent recombination between the species clusters.
Different genes/proteins show different evolutionary histories, due to:
•Limitations of phylogenetic tree reconstruction methods •Horizontal gene transfer •Hidden paralogy
Processes that shape microbial biogeography
•Many attributes vary with an organism's size •Colonization •Speciation (diversification) •Extinction
metapopulation lineages facts:
•Metapopulation lineages do not have to be phenotypically distinguishable, or diagnosable, or monophyletic, or reproductively isolated, or ecologically divergent, to be species. •They only have to be evolving separately from other such lineages.•Definition is not based on methodology, but on their evolutionary fate.•What are these evolutionary forces? •Metapopulation species studies are fewer in environmental microbes, more in pathogens•the frequency of appearance of new phylogenetic branches may be much more continuous within environmental isolates
describe species definitions in microbes in terms of 16s rRNA
•Microbes with 16S rRNAs that are LESS than 98.7% identical are always members of different species, because such strong differences in rRNA correlate with <70% DNA-DNA similarity •But the opposite is not necessarily true, and distinct species have been occasionally described with 16S rRNAs that are >98.7% identical
periodic selection
•Population of cells in the same ecological niche, which would all be out-competed by any adaptive mutant coming from the population •ecotypes are ecologically distinct
quorum sensing
•Production of specific bioactive compounds that, at low concentrations, activate biochemical pathways in one or more target organisms; for signalling •Some autoinducers used in quorum sensing have antibiotic activity at higher concentrations and may also provoke changes in eukaryotic host organisms or tissues
what is the endosymbiont theory?
•Prokaryote/eukaryote dichotomy •Prevalent view in the 70's •Eukaryotic nuclear lineage arose from within the prokaryotes •Mitochondria descend from endosymbiotic Proteobacteria •Plastids descend from endosymbiotic Cyanobacteria
describe how HGT can be detected through phylogenetic conflicts
•Refers to conflicting branching patterns between two gene trees •Usually one of these trees is considered to be an accepted species or a reference tree. •Often the reference tree is assumed to represent the vertical evolution of the organisms that are being analyzed. •Deviations from the branching pattern of the reference tree identify potential HGT events.
steps involved in natural transformation
•Release of extracellular DNA in the environment •Uptake of DNA into the bacterial cytoplasm •Recombination with the host genomeAND/OR •Acquisition of DNA through additive integration
who was Carl Woese(The WoesianRevolution)?
•Rewrote the Tree of Life based on 16S rRNA(1970's-80's) •A grand reconstruction of all of the main events of evolution with a single molecular chronometer
what is microbial biogeography?
•Study of the distribution of microbes over space and time •Where organisms live, at what abundance, and why •Do microbes exhibit geographical structure similar to that of plants and animals? •How they differ from eukaryotes: •Extremely small size •Very large population size •High rates of dispersal
what is competence?
•The ability of bacteria to take up extracellular DNA •Involves approx. 20-50 proteins
describe the coevolution (metabolic) hypothesis IMPORTANT
•The code coevolved with the amino acid biosynthetic pathways, i.e., during the code evolution, subsets of codons for precursor amino acids have been reassigned to encode product amino acids. •The code evolved from an ancestral version that included only simple amino acids produced abiogenicallyand then expanded to incorporate the more complex amino acids in parallel with the evolution of their respective biosynthetic pathways. •The code evolved by subdivision: In the ancestral code, large blocks of codons encoded the same amino acid but were split to encode two amino acids upon the evolution of the respective metabolic pathways.
describe the error minimizing hypothesis IMPORTANT
•The grouping of similar amino acids within the same column of the code table immediately indicates that the code is robust to mutational and translational errors, i.e., that it IS ORGANIZED IN A WAY THAT REDUCES THE DELETERIOUS EFFECTS OF ERRORS •Postulates that the structure of the genetic code was shaped under selective forces that made the code maximally robust, i.e., minimize the effect of errors on the structure and function of the synthesized proteins. •To minimize the impact of coding errors or the likelihood that mutated proteins would be active •Code organization that strongly favors replacement of amino acids with similar ones resulting from single nucleotide substitutions
facts
•The structure of the standard genetic code —that is, the mapping of 64 codons to 20 amino acids and the stop signal—is manifestly regular with respect to multiple criteria. •This non-randomness of the code seems to require an explanation.
competence facts
•Time-limited competence in response to specific environmental conditions such as altered growth conditions, nutrient access, cell density (by quorum sensing) or starvation •Naturally transformable species found in Archaea and Bacteria, including many human pathogens •Enables access to DNA as a source of nutrients or genetic information
Outline of most significant events leading to the LUCA IMPORTANT
•Transition from non-coded to coded peptides gave rise to Darwinian evolution and continue ever since. •Proteins develop from small sized peptides with only a fraction of coded amino acids to formation of motifs and domains with increased coded content. At a later stage the peptides became able to fold and form catalytic centers leading to formation of proteins with fixed 1st and last amino acids. •At the same time standard genetic code expands to cover more codons for at least 20 amino acids. By the time when the first proteins are fully formed the genetic code is established as we know it. •During the period of short peptides and lack of folded peptides/proteins (RNA-peptide world) certain RNAs with catalytic functions were selected (ribozymes) to perform critical catalytic functions. This is time when the ribosome obtained its basic shape. By the time the peptides begun to fold and acquire new enzymatic functions, the ribozymes were already established and could not be replaced, but started to co-exist together with proteins. •The genome size increased proportionally covering the information for all proteins and ribozymes.
rooting by gene duplication
•Use a pair of duplicated genes •Must be universally present •Gene duplication event that predated the last common ancestor •Bacteria diverged first •Note that these are gene trees, not species trees ** look at slide for picture
where have variations to the genetic code been found?
•Variant codes have been found in organelles with tiny genomes and in some parasitic and endosymbiotic bacteria with highly reduced genomes
different levels of selection can act on gene content
•Variation in genome content within a species reflects the ongoing process of gene gain and loss. •Different selective pressures act on these populations and influence gene distribution via HGT.
Questions that remain unanswered in the last 60 years (regarding genetic code):
•Why are the codon assignments what they are? e.g., why is it the case that, for instance, glycine is encoded by GGN rather than, say CCN (which encodes proline)? •Why is the code triplet? •Why are there 20 amino acids encoded by the code table—no more and no less (notwithstanding a few additional amino acids encoded by certain groups of organisms)? •Why is the code highly robust to error? •Why, although highly robust, is the code still far from being globally optimal? •Why is the code universal? And when the code does deviate, why does this occur in some organisms but not others? •What is the probability of finding the same genetic code if we find life outside of Earth?
Salmonella enterica subsp. enterica serovarTyphi (cause of typhoid fever) facts
•descended from a common ancestor that infected humans 10,000-50,000 years ago, but continues to evolve new genotypes •apparent continuity of genetic diversity, which argues against periodic selection •current existence of ancestral haplotypes (H45 in figure) •lack of geographic specificity and many old haplotypes are global in their distribution, indicating multiple events of global spread •local populations consist of a mixture of sensitive and resistant organisms (Periodic selection predicts complete replacement by fitter variants)
antibiotics in agriculture
•livestock, fish (aquaculture), fruit trees •Used to treat disease, promote growth and improve feed efficiency in animals •Antibiotics are used in the absence of acute infection •More widely disseminated due to farm-wide administration of prophylactic antibiotics in feed and water •Effects of the antibiotics extend beyond the site of use: Antibiotics from both urban and agricultural sources persist in soil and aquatic environments •No standardized practice across the world
The challenge remains to determine whether planctomycetes:
•represent a precursor of eukaryotes •the retention of certain characteristics of a proto-eukaryotic LUCA, or •a convergent re-evolution of a eukaryote-like plan
