Term
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Definition
- Discrete segments of DNA that move as a unit from one location to another within other DNA molecules (i.e. transposable elements), can move between different DNA molecules or within same DNA molecule
- Transposable elements are found in all three domains of life
- Move by a process called transposition
- Frequency of transposition is 1 in 1,000 to 1 in 10,000,000 per generation
- idea came before people knew what DNA was
- first discovered in corn
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Term
Two main types of transposable elements in Bacteria
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Definition
- Transposons and insertion sequences
- Both carry genes encoding transposase - enzyme that affects the moving of DNA between sites on the DNA molecule, cut out insertion sequence of transposon and insert it elsewhere in chromosome
- Both flanked by inverted repeats at their ends, anything in between inverted repeats is what actually gets moved around in DNA
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Term
Two main types of transposable elements in Bacteria - insertion sequences
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Definition
- simplest transposable elements, small
- 1000 nucleotides long
- only have one gene - only gene for transposase
- simplest kind of transposable element
- example - IS2
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Term
Two main types of transposable elements in Bacteria - Transposons |
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Definition
- larger than insertion sequences
- can have multiple genes between inverted repeats, one of them has to be transposase by definition, but there can be other ones like antibiotic resistance genes
- more complex than insertion sequences
- transposase moves any DNA between inverted repeats
- Examples are the tn5 and tn10
- transposons can jump and then they can lose the ability to jump anymore, then they'll be stabley integrated into chromosome - no more jumping
- evidence that building up of chromosome through transposable elements that lost the ability to jump, so they remained fixed
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Term
Mechanisms of transposition - Two types
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Definition
- Conservative - transposon is excised from one location and reinserted at a second location - number of transposons stays constant, host DNA and target molecule (where transposon goes) can be same molecule or different molecule, transposon is cut out from original site and inserted into new location
- no copy left behind on original chromosome - conserving number of transposons
- Replicative - a new copy of transposon is produced and inserted at a second location
- original copy of transposon is left behind in original DNA molecule - number of transposons in cell increases
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Term
Using transposons is a convenient way to make mutants
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Definition
- Transposons with antibiotic resistance are often used
- Transposon is genes between inverted repeat sequences, one of these genes can be for antibiotic resistance (like resistance to Ampicillin)
- Transposons is introduced to the target cells on a plasmid that can't be replicated in the cell
- Put transposon into cell, look for cells that are not ampicillin resistant
- Cells that have ampicillin resistance have likely taken up transposon - transposition has happened in those cells
- Cells capable of growing on selective medium likely acquired transposon
- Look for cells that can't make flagella anymore, then map out where transposon is - find genes that are important for making flagella
- Most insertions will be in genes that encode proteins
- You can then screen for loss of function and determine insertion site
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Term
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Definition
study of the entire genetic content of an organism - all genes
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Term
What value is the sequence of a bacterial genome?
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Definition
1) provides direct access to the functional biology of a bacterium, by identifying each gene by comparisons with the genomes of other bacteria - we have powerful resources, computers, filled with genomes of many organisms, through comparing sequence, we can predict what genes must be there and what proteins must be encoded 2) comparative analysis of the structure of bacterial genomes (circular vs. linear chromosomes, number of chromosomes, their gene content and gene order, and the sequences of the genes) reveals historical (evoluationary) relationships among bacteria - promoter sequences - consensus motif - comparison of how close the sequences are |
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Term
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Definition
- use rRNA to make comparisons of different organisms and see what organisms are present in environment, even if we couldn't grow them
- come up with by Carl Woese
- proteins, gene sequences are very conserved over long periods of time
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Term
>2000 bacterial, Archaeal, and viral genomes sequenced/in progress
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Definition
- RNA virus MS2 - first genome sequenced in 1976, has 3569 bp
- Haemophilus influenza - first cellular genome sequenced in 1995, has 1,830,137 bp
- Average bacterial gene is 1000 bp (1 kb)
- As genome size increases, gene content proportionately increases, but not always
- holds true for microorganisms, but not always true for euks
- Euks have the distinction of having large amounts of non-coding DNA
- As euk genome get large, the number of open reading frames does not always proportionately increase
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Term
Smallest cellular genomes
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Definition
- belong to parasitic or endosymbiotic bacteria/archaea
- Archaeal Obligate parasites range from 490 kbp (Nanoarchaeum equitans) to 4400 kbp (Mycobacterium tuberculosis)
- Endosymbionts can be even smaller e.g. 160 bp genome of Carsonella ruddii - smallest on planet
- can have such a small genome because its within cell so it can parasitize host cell genes and let host cell perform some of the necessary functions for it, releases it from the need to have all genes in its own genome
- Minimum number of genes for viable cell - 250-300 genes
- Largest bacterial genomes comparable to those of some euks
- Sorangium cellulosum (Bacteria)
- largest prok genome to date at 12.3 Mbp
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Term
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Definition
- Science that applies powerful computational tools to DNA and protein sequences
- enter in gene sequences into computer and get all organisms that have that sequence
- For the purpose of analyzing, storing, and accessing the sequences for comparative purposes
- compare YFG to any other gene sequence in database and tel you which are most similiar to YFG
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Term
Complement of genes in a particular organism defines its biology but genomes are also molded by an organisms lifestyle |
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Definition
- Many gene can be identified by sequence similarity to genes found in other organisms (comparative analysis)
- Comparative analyses allow for prediction of metabolic pathways and transport systems - don't have to grow organism - put together map of what organism might look like
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Term
What can you learn just from gene sequence comparisons?
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Definition
Thermotoga maritima - hot springs - can learn all about organism by putting sequence of its genome into computer and then it will tell us all things that are similiar to other organisms
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Term
Gene distribution in bacteria
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Definition
- Metabolic genes typically most abundant class - like housekeeping genes
- DNA replication and transcription genes make up minor fraction of genome
- Nontranslated RNA genes are typically prevalent e.g. rRNA, tRNA, small regulatory RNAs (antisense RNA)
- lots of genes are unknown, though - most of genes in E.Coli we don't really know about
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Term
Some gene sequences are hard to identify by comparison analysis
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Definition
- number of genes with role that can be clearly identified in a given genome is 70% or less of total ORFs detected - lots of hypothetical proteins
- Hypothetical proteins - uncharacterized ORFs - proteins that likely exist but whose function is presently unknown - its not similiar to anything else we know
- probably its non-essential because if we take it out, organism is fine - not needed to live
- In E.Coli, many predicted to encode regulatory or redundant proteins
- Inaccuracies in some annotations are problematic
- As many as 10% of annotated genes are incorrectly annotated
- someone labeled gene sequence wrong and put into database - human mistakes in labeling genes
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Term
Percentage of an organism's genes devoted to a specific cell function is to some degree a function of genome size |
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Definition
- for smaller genomes - greater proportion of genome is dedicated to translation, DNA replication and a smaller proportion is dedicated to energy generation, signal transduction
- As size of genome increases, smaller proportion of genes is dedicated to translation and replication but are more dedicated to signal transduction
- Replication is a conserved process - highly similiar across species - just a few ways of doing it, once organisms figure out how to replicate their DNA, they're only gonna replicate it one way, not gonna invent new ways, only need a few genes to do that process
- As space in genome grows, you need more ways to communicate between the cell - increase in signal transduction machinery
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Term
Gene Distribution in Bacteria vs. Archaea |
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Definition
- Archaea typically devote a higher percentage of their genomes to energy and coenzyme production than do bacteria
- Archaea contain fewer genes for carb. metabolism or cytoplasmic membrane functions than do bacteria
- Lifestyle influences this
- Archaea - extremophile - more ways to do energy conversion in environment
- Most genes still unknown
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Term
Endosymbiotic cell theory
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Definition
- organelles in euks arise from bacterial ancestors
- only bacteria that were origin or organelles, not archaea
- There was an organism that was like a euk because it developed a nucleus
- This nucleated structure at one time engulfed an aerobic heterotroph, which became mitochondria
- Later on, that organism diverged. Some went on to be ancestors of heterotrophic euks while others engulfed photosynthetic bacterium (cyanobacterium, probably), this one became the ancestor of algae
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Term
How do we know Endosymbiotic Theory is valid?
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Definition
- Mitchondria and chloroplasts contain a small genome (circular)
- The genome containes necessary machinery for protein synthesis, including ribosomes, tRNAs, and all other components necessary for translation formation of functional proteins
- Many genes in the nucleus encode proteins required for organelle function e.g. translational machinery, energy generation that get imported into organelle when needed
- many genes that were on the ancestral mitochondria or chloroplast were moved onto host chromosome
- greatly reduced genome, very small
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Term
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Definition
- The entire complement of RNA produced under a given set of conditions
- Hybridization techniques can be used in conjunction with genomic sequence data to measure gene expression
- Look at entire complement of RNA that can be produced under a certain set of conditions
- measure of gene expression
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Term
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Definition
- Small solid-state supports to which genes or portions of genes are fixed and arrayed spatially in a known pattern
- ways of using ability of nucleic acids to form hybrids (Base pairs) to measure what RNAs are present in sample
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Term
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Definition
- DNA from sequence of organism of interest immobilized on plate, everywhere where you see something lighting up - some RNA from sample bound and made DNA:RNA hybrid - fluorescence - light indicates where that hybridization was able to occur - detect what RNA is being expressed from organism you are interested in
- All the RNA that is being expressed - TRANSCRIPTOME
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Term
What can we learn from microarray experiments?
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Definition
- Global gene expression - put organism in glucose, lactose genes not made
- Expression of specific groups of genes under different conditions - just look at expression of specific subset of genes under different conditions
- Expression of genes with unknown function; can yield clues to possible roles - put DNA onto Gene Chip of unknown genes, ask what conditions will make those regions light up - clue as to function of genes
- Comparison of gene content in closely related organisms
- ID of specific organisms
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Term
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Definition
Global view - Proteomics - genome wide study of the structure, function, and regulation of an organism's proteins - what proteins are present at any given moment
- Metabolome - the complete set of metabolic intermediates and other small molecules produced in an organism - what metabolites present at any given time, globally
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Term
How close is close enough? How close is the sequence of one gene to another gene?
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Definition
- Proteins with >50% sequence identity (nucleic acid) between two genes typically have similiar functions
- Proteins with >70% sequence identity almost certainly have similiar functions
- Is this talking about DNA or polypeptide sequence? - they aren't always the same - if two proteins have >70% similarity between their amino acids - they most likely have similiar functions but they may not be evolutionarily related because even though there amino acid sequences are the same, their DNA sequences might be different b/c of functional redundancy of codons - 64 codons for only 20 amino acids - may ways to make the same amino acid
- Amino acids could be very similiar but DNA that encodes those amino acids can be really different - must look at DNA to determine evolutionary relationships
- Protein domains
- Distinct structural modules within proteins
- Have characteristic functions that can reveal much about a protein's role, even in the absence of complete sequence homology
- Helix turn Helix DBD - binds DNA at inverted repeats
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Term
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Definition
- Homologous - related in DNA sequence to an extent that implies common genetic ancestry, for something to be homologous to something else, that means they have a common ancestor, doesn't mean similiar, even if they have same amino acid sequences, there DNA sequences might be different
- Gene families - groups of gene homologs e.g. gene family of ABS sugar transporters, all came from common ancestor
- Paralogs - genes within an organism whose similiarity to one or more genes in the same organism is the result of gene duplication, genes in an organism that are similiar to each other because of a gene duplication, that gene duplicated and now in that chromosome you have two copies of the gene, one of them was able to mutate and evolve away from the first but they are still related - homologous and paralogs
- orthologs - genes found in one organism that are similiar to those in another organism but differ because of speciation - ex. two different organisms' flagella genes that are homologous (have common ancestor) but they are different from each other b/c they have undergone speciation, evolved away from each other
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Term
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Definition
- Gene duplications thought to be mechanism for evolution of most new genes - extra copy of gene appears on chromosome, can then mutate
- Deletions can eliminate gene no longer needed - use it or lose it
- Gene analysis in the 3 domains of life suggests that many genes present in all organism have common evolutionary roots (homologous), peptidly transferase is homologous across all species
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Term
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Definition
- transfer of genetic information b/w organisms, as opposed to vertical inheritance from parental organisms
- conjugation - horizontal gene transfer - b/w diff. organisms
- may be extensive in nature, may cross phylogentic domain boundaries, happens a lot with grasses, pollen can be transferred b/w diff. species of grass - gene flow b/w species, transduction via viruses - bring genes between Gram negative bacteria and another unrelated Gram negative bacteria
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Term
Detecting Horizontal Gene Flow
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Definition
- Presence of gens typically found only in distantly relates species, all of nearest relatives lack the gene, but there it is over in less-related Archaeal organism - perhaps Horizontal transfer happened
- Presence of DNA with GC content or codon vias that differes significantly from remainder of genome
- GC content - every organism has own distinct level of GC base pairs - characteristic of certain organism
- little islands of DNA that have eratically different GC content versus everything else - indication of Horizontal Gene transfer
- Hozintally transferred genes typically encode non-core metabolic functions
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Term
How to do horizontal transfer
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Definition
- Transposons may transfer DNA b/w diff organisms
- Transposons may also mediate large-scale chromosomal changes within a single organism
- Happens because of multiple insertion sequences - transposon can go to all of these insertion sequences - create many changes in chromosome
- Recombination among identical insertion sequences can result in chromosomal rearrangements
- flip DNA around, deletions, inversions, translocations
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Term
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Definition
- chromosomal islands - region of bacterial chromosome of foreign origin that contains clustered genes for some extra property such as virulence or symbiosis
- Pathogenicity islands - chromosomal islands containing genes for virulence - created by Horizontal gene flow, can also be on plasmids
- Chromosomal islands believed to have foreign origin based on several observations
- Extra regions often flanked by inverted repeats - like transposons
- Base composition and codon usage in chromosomal islands often differ from rest of genome - number of GC base pairs distinct from rest of genome
- often found in some strains of a species but not others
- Chromosomal islands contribute specialized functions not essential to growth
- virulence
- biodegradation of recalcitrant compounds like hydrocarbons and herbicides
- Symbiosis
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Term
Pan/Core concept: bacterial species consist of two components
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Definition
- hard to define species - lots of DNA moving around
- Core genome - shared by all strains of the species
- Pan genome - includes all the optional extras present in some but not all strains of the species
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Term
Genomics of unculturables |
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Definition
- can't culture, can't grow in lab
- Metagenome
- the total gene content of the organisms present in the environment
- several environments have been surveyed by large-scale metagenome projects e.g. acid mine run-off waters, deep sea sediments, fertile soils - tell what species are present
- the human microbiome - most of the unique genes in are body are not human, they are microbes - determine the total genetic complement of human genome with all bacterial sequences present
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Term
| Viruses are more prevalent than bacteria in the environment |
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Definition
- Most are bacteriophages and have populations that turn over rapidly
- Most of the genetic diversity on earth thought to reside in viruses
- Most virus genes are uncharacterized and show little or no sequence similarity to known genes
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