BIOLOGY 207: LECTURE 16
38 Cards in this Set
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What is the genome?
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The _____ is the full complement of an an organism's genetic information chromosome(s) and plasmid(s)
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What is microbial genomics? What does it identify and provide?
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_______ is the whole sequence and analysis of a bacterium's genome (identification of genes present, organization, function and expression)
Provides definitive insight into organism's function, interaction w/ environment and evolutionary history
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When and how did microbial genomics begin?
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_____ began in 1995 with report of sequence of genome of Haemophilus influenzae strain Rd, species of bacteria that caused most cases of juvenile meningitis in U.S. before vaccine developed in 1990
one of youngest disciplines in microbiology
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What is the genome size of H. influeanzae (vs. e coli) and what is its significance?
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Genome size of _____ is 1.8 Mb, 3 x smaller than E. coli
was first genome sequenced of free living organism?
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What did success w/ H. inluenzae demonstrate as a method for sequencing large genomes?
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The _________ demonstrated the effectiveness of "whole genome shotgun sequencing" as a method for ____________
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Whole genome shotgun sequencing process
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start by growing up culture of bacterial strain of interest, extract+ purify its chromosomal DNA; shear the DNA mechanically into small fragments; clone fragments into plasmid; using sequence primers complementary to plasmid at positions flanking fragment insertion site, sequence fragment…
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What is the plasmid vector of the fragments of DNA form in whole genome shotgun sequencing?
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The __________ is now a library of the DNA of the strain of interest (whole genome shotgun sequencing)
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What followed the sequencing of the H. influenzae genome? When completed
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Mycoplasma genitalium followed after the sequencing of ______
completed in 1995
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What is mycoplasma genitalium? Genome size? Chromosome composition?
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____ is a pathogen that causes human nongonococcal urethritis
Its genome size is 0.58 Mb, one of the smallest bacterial genomes known
It is one circular chromosome with 482 protein encoding genes
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how may total genomes have been sequenced so far? how many bacteria? archaea? eukarya? viruses?
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total - 51,176
Bacteria -37,192
Archaea-926
Eukarya-8,660
Viruses- 4,398
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What is GOLD?
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Genomes on-line database
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For each genome, what does the annotation do and what does it provides?
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For each genome ___ reads the blueprint of the hundreds of interactive processes and provides insight into the organism's life style
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What types of chromosomes are there are and what are some examples of bacteria of each
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most bacteria have one circular chromsome (like escherichia coli) (plus plasmids)
some have two circular chromosomes one larger one smaller plus plasmids like Aliivibrio, vibrio, photobacterium
some have one ircular and one linear chromosome (plus plasmids)
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How much of the genome is non-coding? What is the spacing on genomes like?
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bacterial genes are densely packed on the chromosome, very little of the genome is non-coding
Very litle of the genome is non-coding (8-10%)
very little is intergenic space and much of that probably is binding sites for RNA polymerase and transcriptional regulatory proteins
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How much of the genome is coding? What does that tell us?
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typically 90% or so of the genome is coding
tells us each organism has a set of genes fitted to it
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What are orfs?
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____ = open reading frame (i.e. "gene")
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How many orfs on average have no known function? What does that tell us?
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A high percentage of orfs,, 43% on average, have no known function
tells us that most of genes haven't been studied in that way of looking at a gene sequence by sequence
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23% of the orfs average, appear to be _______ what does that tell us?
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_____ of the orfs on average, appear to be unique to each species
tells us that each org has a set of genes fitted to it
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Relationship of bacterial genomes and size
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bacterial genomes vary in size
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Carsonella ruddi size, ORFs, biology
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0.16 Mb 182 ORF
Degenerate aphid endosymbiont (lives within body or cell of animal)
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Escherichia coli size, ORFs, biology
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4.5 Mb 4288 ORF
Gram negative genetic model, free-living
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Mycoplasma gentialium size, ORFs, biology
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.58 Mb
470 ORF
Parasite
Smallest nonsymbiotic bacterial genome
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Sorangium cellulosum size, ORFs, biology
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13.0 Mb
9367 ORF
Free living
Myxobacterium that forms multicellular fruiting bodies
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Genome length of human vs amoeba vs cockroach
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cockbroach bigger than ameoba bigger than human
size not necessarily indication of genome size
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What does genome size correlate directly with? What does that mean?
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_____ correlates directly with the number of ORfs
bigger DNA --> more genes
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What can be told through annotation about the gene? What does the identification depend on?
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_______, the kind of gene and its function often can be identified. identification depends on what gene have already been identified in other bacteria
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Variation of genes responsible for essential information functions _______. What does this mean?
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Genes responsible for _________ (DNA metabolism, trnascription, protein synthesis) do not vary much btwn bacteria
Means that perhaps there is a minimal number of these essential genes necessary for life
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Bacteria that can live free of host cells (examples, where live?) vs parasitic genes.
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Bacteria that can ______ e.g. E. coli B. subtilis in complex and variable environemnts have more operational or housekeeping genes than do bacteria that are more _______
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Significance of obligate parasitic genes vs free living bacteria; What can we say abt symbionts?
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Obligate parasitic forms apparently depend on host for many of cellular building blocks (nutrients) that "free living" bacteria have to make for themselves
One can say that generally, bacteria that are obligate parasites or obligate symbionts can get rid of genes for many biosynthetic …
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Pseudomonas aeruginosa (describe, fraction ofgenes dedic. to transcript regulation)
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_______ is a free living prototroph, able to colonize many different kinds of habitats
8.4% of genome encodes liely transcriptional regulators
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Helicobacter pylori (describe, fraction ofgenes dedic. to transcript regulation)
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____ is a human pathogen that is found apparently on line human stomach and under small range of environmental variables there
1.1% of genome encodes likely transcriptional regulators
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Correlation btwn genome size, number of ORfs and life style
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Larger genomes have more OFRs
Bacteria that can live free of host cells
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Examples of bacteria that live free of host cells, environments they habitat, number of operational genes
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Escherichia coli (mammalian intestinal tract, freshwater, surfaces of plants, foods)
Bacillus subtiilis (soil bacteria) in complex and variable environments have MORE operational "housekeeping" genes than do parasitic baceteria
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Why Obligately parasitic genes have fewer housekeeping genes
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____ are thought to have evolved into dependency on host for many of necessary nutrients that "free living" bacteria have to make for themselves
over time, obligately parasitic bacteria have lost genes neccessary for existence independent of host by giving up genes for many biosyntheti…
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Treponema pallidum (description, how much known about it, genome size)
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_____ is causative agent of syphilis
grows well only in the human body
very hard to study (bc grow very poorly in media/culture)
little known about its metabloism or how it avoids host defeneses
no vaccine develped
Genome size - 1.14Mb
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What does genome sequence reveal about metabolism of Treponema pallidum?
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Reveals that it is metabolically crippled
Although can use carbohydrates for energy generation (glycolysis, substrate level phsophrolyation) lacks CAC cycle and oxidative phosphorylation (whihc carry out oxidation of organic cabon to CO2 w/ lots of ATP generation as consequence
Therefo…
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If humans become extinct, what will happen to T. pallidum
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cannot live on its own, will die
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____ account for 80% of the bacterial genomes sequenced What are they?
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three phyla account for _______
Protobacteria
Firmicutes
Actinobacteria
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BIOLOGY 207: LECTURE 25