Transcript Solid Waste in History

Microbial Ecology and
Environmental Genomics
The 2nd Week
Introductions to
- Principles of Microbiology
- Molecular Biology of Microorganisms
Basics: Microbiology
The Cell (living entity)
• Growth and self-reproduction
• Highly organized and selectively restrict what crosses
their boundaries (a lower entropy compared to their
environment)
• Composed of major elements (C, N, O, and S, in
particular)
• Self-feeding of elements, electrons, and energy
Basics: Microbiology
Eukaryotic cell
Prokaryotic cell
Basics: Microbiology
Essential Cell Components
• Cell membrane: a barrier between the cell and its
environment (selectively transporting elements, electrons,
and energy)
• Cell wall: a structure member that confers rigidity to the
cell and protects the membrane
• Cytoplasm: most of the inside of the cell
• Chromosome: stores the genetic code for the cell’s
heredity and biochemical functions
• Ribosomes: convert the genetic code into working
catalysts that carry out the cell’s reactions.
• Enzymes: biological catalysts
Organism Classification
Taxonomy
• Science of classification
• Based upon observable properties (phenotypes) including
morphology and transformation
• Traditional way of organism classification
Phylogeny
• Science of classification
• Based upon evolution history (small subunit of rRNA,
functional gene sequencing, genome sequencing)
• New way of organism classification
Basics: Microbiology
Naming bacteria/archaea
• Escherichia coli O157:H7
• Pseudomonas aeroginosa PA01
• Burkholderia xenovorans LB400
RULE: Genus (italic) species (italic) strain
(ref. the International Code of Nomenclature of Bacteria)
Species: the basic taxonomic unit
Genus: population unit
Basics: Microbiology
Characteristic
Membrane-enclosed nucleus
Muramic acid in cell wall
Chlorophyll-based photosynthesis
Methanogenesis
Reduction of S to H2S
Nitrification
Denitrification
Nitrogen fixation
Synthesis of poly-beta-hydroxylakanoate
carbon storage granules
Sensitivity to chloramphenicol,
streptomycin, and kanamycin
Rebosome sensitivity to diphtheria toxin
Bacteria
Archaea
Eukarya
Absent
Present
Yes
No
Yes
Yes
Yes
Yes
Yes
Absent
Absent
No
Yes
Yes
No
Yes
Yes
Yes
Present
Absent
Yes
No
No
No
No
No
No
Yes
No
No
No
Yes
Yes
Source: Madigan, Martinko, and Parker, 1997
Phylogenetic tree of life as determined from small
subunit of ribosomal RNA sequencing (C. R. Woese)
-0.1
Bacteria
G+ Proteo- Cyano-
Eucarya
Mouse
Fruit fly
Plant
HGT
-1.0
HGT
-2.0
Origin of oxygenic
photosynthesis
2.3
Archaea
Crenarchaeota
1.0
1.5
Amito
-chondriate
Euryachaeota
2.1
-3.0
-4.0
Last common ancestor
Origin of Earth (4.5 billion years)
3.8
Chemical evolution/
Prebiotic synthesis of
biomolecules
Basics: Microbiology
Environmentally important microorganisms
• Bacteria and Archaea (Prokaryotes): detoxification,
diseasing-causing, biochemical cycles in nature
• Algae (Single-celled Eukaryotes) and Cyanobacteria
(Prokaryotes): water quality problem, toxin-producing.
• Single celled protozoa (Eukaryotes): bacteria eater,
disease-causing
• Fungi (multi-cellular Eukaryotes): detoxification
Prokaryotes
Bacteria
Are among the smallest of the entities that are generally
agreed to be living.
Ubiquitous (everywhere)
Able to transform a great variety of inorganic and organic
pollutants into harmless minerals (which is recycled
back into the environment) => Beneficial to human
Often cause disease or are responsible for many of the
plagues of the past and for mjor sickness and misery
=> Threatening human health
Archaea (later…)
Bacteria
Morphology
Coccus (spherical shape)
Streptococci
Staphylococci
Sarcina (packets of eight)
Bacillus (cylindrical rod shape)
Chains of bacilli
Spirillum (helical shape)
Bacteria
Size and some number for bacteria
•
•
•
•
0.5-2 μm (width) x 1-5 μm (length)
0.5-5 μm (Diameter for Cocci)
1012 cells per gram of dry solid weight
Surface area: 12m2/gram
Bacteria
Cell structure
Cell wall: peptidoglycan (G-negatives have a
higher content of lipopolysaccharide while Gpositives teichoic acids)
Cytoplasmic membrane: phospholipid bilayer,
semipermeable, membrane-bound electrontransport enzymes (cytochromes), selective
material transport
Cytoplasm: consist of water, dissolved nutrients,
enzymes, proteins, and nucleic acids (RNAs and
DNAs), and ribosomes (protein-RNA)
Inclusion: storage for food or nutrients (e.g. PHB,
fatty materials, or sulfur accumlation)
DNA: chromosome, plasmid (mobile)
RNA: mRNA, tRNA, rRNA
Endospores (e.g. Bacillus, stress response)
Capsule or slime layer: floc formation
Flagella: chemotaxis, phototaxis
Fimbriae and pili: attachment, involved in
conjugation
Bacteria (why C5H7O2N?)
Chemical composition
Constituent
Percentage
Water
Dry Matter
Organic
C
O
H
N
Inorganic
P2O5
K2O
Na2O
MgO
CaO
SO3
75
25
90
45-55
22-28
5-7
8-13
10
50
6.5
10
8.5
10
15
Macromolecular composition
Macromolecule
%a
%b
Molecules
per cell
Total
Proteins
Carbohydrates
Lipids
DNA
RNA
100
50-60
10-15
6-8
3
15-20
100
55
7
9.1
3.1
20.5
24,610,000
2,350,000
22,000,000
2.1
255,500
NOTE a: dry weight (Rittmann and McCarty)
b: dry weight, data from E.coli and S. typhimurium
[Madigan, Martinko, and Parker (1997)
and G. C. Neidhardt et al (1996)]
E.coli dry weight for actively growing cells is
about 2.8x10-13 g
Trace heavy metals in enzymes
molybdenum (N2 fixation)
nickel (anaerobic methane production)
cupper (methane oxidization)
Prokaryotic Reproduction
Binary fission (normal way of multiplication)
Bacteria’s normal way to reproduce themselves.
After reproduction, the parent cells no longer exists, and the two
daughter cells normally are exact replicates (i.e., clones) of each
other, both containing the same genetic information as the parent.
(Joon’s question…NO AGING?)
Asexual reproduction
Replication: chromosome (genomic DNA) is replicated and divided
into each daughter cell.
Filamentous growth
 Norcardia species produce
Replication of
chromosome
extensive filamentous growth
Formation of long, branching,
non-dividing filaments, containing
multiple chromosomes. (Multicellular???)
In stressed conditions, some of
these species form spores (some
Streptomyces and many molds)
Prokaryotic Reproduction
Budding division
 Asymmetric creation of a growing bud, on the
mother cell.
 The bud increases in size and eventually severed
from the parental cell.
 After division is complete, the mother cell reinitiates
the process by growing another bud.
 Yeast and some bacteria (Caulobacter is one
example) use this form of division.
Sexual reproduction via conjugation
 Some bacteria transfer plasmid (not chromosome) into
other bacteria using conjugation process (cf. Horizontal
gene transfer)
 Conjugation requires direct contact between two cells.
 Conjugation results in replication of genetic information.
 And then multiplication can occur….
 Conjugation often occurs between same species as well
as between different species (even different genus levels).
Conjugation
Binary fission
Prokaryotic Growth
Prokaryotic growth curve
Calculation of growth rate
Growth rate: dN/dt = k * N (exponential
growth)
Integration: N2 = N1 * EXP[k*t]
Growth rate constant: k = ln(N2/N1)/(t2-t1)
here X : biomass or cell number
Xo: initial biomass or cell number
t2 : 2nd measurement time point
t1: 1st measurement time point
Example
The value of growth rate possibly is
influenced by the way of quantifying
growth (i.e., cell number counts vs.
biomass).
Bacteria
Energy and carbon-source classes of bacteria
Phototrophs (use light as energy source)
- Oxygenic phototrophs use light to convert water into O2 and H2, the
electron sources. This is similar as plants do, and is dependent the type of
chlorophylls.
- Anoxygenic phototrophs live in the absence of O2 They use light to extract
electron sources from reduced sulfur compounds (H2S), H2 or organic
compounds (succinate or butyrate). One example is conversion of H2S into
H2 and S.
Chemotrophs (use chemicals as energy or carbon sources)
- Chemoorganotrophs (organic chemicals)
- Chemolithotrophs (inorganic chemicals)
- Autotrohs (use inorganic carbon such as CO2 for cell synthesis)
- Heterotrophs (use organic carbon for cell synthesis)
Bacteria
Environmental conditions for growth
• Temperature
•
Psychrophile (-5 to 20oC)
Mesophile (8 to 45 oC);
Thermophile (40 to 70oC)
Hyperthermophile (65 to 110 oC)
Aerobes (respiration with oxygen);
Anaerobes (respiration in the absence of
oxygen);
Aerotolerant anaerobes (can grow in the
presence of oxygen but cannot use
oxygen);
Facultative aerobes (do both aerobic and
anaerobic respiration);
Microaerophiles (can grow in presence of
minute quantities of oxygen molecules)
•
pH
Typically, bacteria have a narrow pH range of
for growth (6 to 8)
For some species, the operating range is
quite broad.
Acidophilic bacteria (some
chemolithotrophs oxidizing sulfur or iron
for energy at highly acidic conditions.)
•
Oxygen
Salts
Halophiles (grow best under salt conditions
similar to seawater, 3.5% NaCl)
Extremehalophiles (live well in a saturated
NaCl, 15-30%)
Bacteria
Characteristics of 12 phylogenic lineages of bacteria
Aquifer/Hydrogenobacter: Hyperthermophilic, chemolithotrophic
Thermotoga: Hyperthermophilic, chemoorganotrophic, fermentative
Green nonsulfer bacteria: Thermophilic, phototrophic and nonphototrophic
Deinococci Some thermophiles, some radiation resistant, some unique spirochetes
Spirochetes: Unique spiral morphology
Green sulfur bacteria: Strictly anaerobic, obligately anoxygenic phototrophic
Bacteroides-Flavobacteria: Mixture of types, strict aerobes to strict anaerobes, some are
gliding bacteria
Planctomyces: Some reproduce by budding and lack peptidoglycan in cell walls, aerobic,
aquatic, require dilute media
Chlamydiae: Obligately intracellular parasites, many cause diseases in humans and other
animals.
Gram-positive bacteria: Gram-positive, many different types, unique cell-wall composition
Cyanobacteria: Oxygenic phototrophic
Purple bacteria (Proteobacteria): Gram-negative; many different types including
anoxygenic phototrophs and nonphototrophs; aerobic, anaerobic, and facultative;
chemoorganotrophic and chemolithotrophic
Proteobacteria (purple bacteria)
Pseudomonads (belonging to α,β, andγ groups)




Pseudomonas, Commamonas, Burkholderia
A broad classification of microorganisms important in organic degradation
Straight or slightly curved rods with polar flagella.
G-negative chemoorganotrophs that show no fermentative metabolism
Sulfate
Alpha: Rhodospirillum*, Rhodopseudomonas*, Rhodobacter*, Rhodomicrobium*,
Rhodovulum*, Rhodopila*, Nitrobacter, Agrobacterium, Aquaspirillum,
Hyphomicrobium, Acetobacter, Gluconobacter, Beijerinckia, Paracoccus,
Pseudomonas (some species).
Beta: Rhodocyclus*, Rhodoferax*, Rubrivivax*, Spirillum, Nitrosomonas, Sphaerotilus,
Thiobacillus, Alcaligenes, Pseudomonas, Bordetella, Nesisseria, Zymomonas
Gamma: Chromatium*, Thiospirillum*, other purple sulfur bacteria*, Beggiatoa,
Leucothrix, Escherichia and other enteric bacteria, Legionella, Azotobacter,
fluorescent Pseudomonas species, Vibrio
Delta: Myxococcus, Bdellovibrio, Desulfovibrio and other sulfate-reducing bacteria,
Desulfuromonas
Epsilon: Thiovulum, Wolinella, Campylobacter, Helicobacter
* Phototrophic representatives (SOURCE: Madigan, Martinko, and Parker, 1997)
TEA
Oxygen and nitrate
AMD, Corrosion
Major grouping of proteobacteria
Archaea
Archaea versus Bacteria
 Bacteria generally have peptidoglycan in cell walls but Archaea do
not.
 Bacterial membrane fatty acids tend to be straight chained (ester
linkages), while the archaeal membrane lipids tend to be long-chained,
branched hydrocarbons (ether linkages).
 Bacterial RNA polymerase is of single type with a simple quaternary
structure, while Archaeal RNA polymerase are of several types and
structurally more complex.
Meaning of studying Archaea in Biotechnolgy
Methanogens (in Euryarchaea group) convert hydrogen and acetate
into methane, a useful energy source.
Extremophiles (Thermophiles, Halophiles, and Acidophiles) are
common in Archaea
=>Useful for biological treatment of industrial wastewaters that may
contain extremes in salt concentration or temperature
Archaea
Major groups and subgroups
 Crenarchaeota: Desulfurococcus, Pyrodictium, Sulfolobus,
Thermococcus, Thermoproteus
 Korarchaeota: Hyperthermophilic Archaea (have not yet been obtained
in pure culture)
 Euryarchaeota: Archaeroglobus, Halobacterim, Halococcus, Halophilic
methanogen, Methanobacterium, Methanococcus, Methanosarcina,
Methanospirillu, Methanothermus, Methanopyrus, Thermoplama
Eukarya
Of interest in environmental biotechnology
 Fungi: (1) the primary decomposers in the world; (2) decompose a great variety of
organic materials that tend to resist bacterial decay (decomposition of lignin, leaves,
dead plants and trees, and other lignocellulosic organic debris via peroxidase pathways);
(3) decomposition of dry organic matter (stabilization of sludge and refuse); (4) favor soil
environment, high organic concentration, and drier and more acidic conditions
compared to prokaryotes); (5) unfortunately, their detoxification is slow
 Algae: (1) important in surface water quality control; (2) produce organic matters
using light (phytoplankton); (3) oxygenic photosynthesis is good for water quality and
wastewater treatment; (4) too much algae growth cause tastes and odors in water
supplies, clogging problems in water treatment plants; decreased clarity of lakes;
increased sedimentation in lake; (5) a balanced population of algae is required.
 Protozoa: (1) common members in aerobic and anaerobic wastewater treatments; (2)
also are observed in most freshwater and marine habitats; (3) feed on bacteria and
small organic particulate matter (polishing effluent from wastewater treatment plants); (4)
Indicate the presence of toxic materials
 Multicellular microscopic Eukarya: rotifers, nematodes, and other
zooplankton
Viruses
Major characteristics
Not considered to be “living” entities
Replicated only when in association with a living cell
Consisting of nucleic acid (DNA or RNA) surrounded by protein
15-300 nm (Smallpox 200-300 nm; Herpes simplex 100 nm;
Influenza 100 nm; Adonovirus 75nm; Bacteriophase 80nm;
Tobacco mosiac virus 15 x 280 nm)
 Bacteriophages: virus infects prokaryotes
 Phages are prevalent in biological
wastewater treatment systems
 A virus infection occurs quite rapidly
(within about 25 min, 200 new phases
can be produced.)




Infectious Diseases
Microorganism
Class
Group
Organism name
Virus
Viscerotropic
Coxsackie virus
Norwalk virus
Rotavirus, Echovirus
Hepatitis A virus
Polio virus
Campylobacter jejuni
Helicobacter pylori
E. Coli O157:H7
Legionella pneumophilia
Salmonella typhi
Shigella dysenteriae
Vibrio cholerae
Gambierdiscus toxicus
Gonyaulax catanella
Pfiesteria piscicida
Giardia lamblia
Entamoeba histolytica
Cryptosporidium parvum
Bacteria
(Proteobacteria)
Algae
Protozoa
Disease and symptoms
Viscerotropic
Neurotrophic
Epsilon
Epsilon
Gamma
Gamma
Gamma
Gamma
Gamma
Dinoflagellate
Dinoflagellate
Dinoflagellate
Mastigophora
Sarcodina
Sporozoa
Gastroenteritis
Infectious hepatitis
Poliomyelitis
Gastroenteritis, diarrhea, etc
Peptic ulcers
Diarrhea, hemorrhagic colitis
Respiratory illness
Typhoid fever, blood in stools
Dysentery, blood in stools
Cholera
Ciguatera fish poisoning
Shellfish poisoning
Memory loss, dermatitis
Giardiasis, diarrhea, bloating
Amebiasis, bloody stools
Cryptoporidiosis, diarrhea
Reading Assignments
For the Current Lecture
- Environmental Biotechnology; Ch.1, pp. 1-42
- Brock Biology of Microorganisms 12th; Ch.1 & Ch.2
Overview of Biology Systems
Ecosystem
Communities
Populations (at Genus level)
Cellular level
Subcellular level
gene (DNA) => mRNA => protein => enzyme =>function
rRNA
tRNA
Bioremediation 2006 March 17
Park Joonhong (C)
Information flow from the gene to the working
enzyme catalyst
Deoxyribonucleic acid (DNA)
(Chromosome, plasmid)
Transcription
Messenger RNA
(ribonucleic acids)
A gene
Replication
Translation by the
ribosome, containing
ribosomal RNA
Amino acid – transfer RNA
Bioremediation 2006 March 17
Park Joonhong (C)
Protein enzyme
Unit component of nucleic acids
B ase
OH
5
HOCH2
H
O
C 4
H
3
C 1
H
C
H
C 2
OH
OH
c.f.)
Ribose
Ribose
unit unit
B ase
OH
5
HOCH2
H
O
C 4
H
3
C 1
H
C
H
C 2
OH
O
HH
c.f.) Riboseunit
unit
Deoxyribose
Bioremediation 2006 March 17
Park Joonhong (C)
Deoxynucleotide unit
O-
Ester bond formed
with release of H2O
Base
O- P
O
O
H
5
CH2
O
C 4
H
3
Deoxyribose
Glycosidic bond
formed with release
of H2O.
C 1
H
C
H
C 2
OH
H
Monophosphate deoxynucleotide
Bioremediation 2006 March 17
Park Joonhong (C)
Adenine (A)
N
O
Thymine
NH2
Hydrogen bond
H3C
N
H
NH
N
H
N
H
H
A-T compliment bond
N
O
H
H
Cytosine (C)
O
Guanine (G)
NH2
Hydrogen bond
H
N
NH
NH
H
N
H
H
NH2
N
H
G-C compliment bond
Purine
Purine
bases
N
O
H
H
Pyrimidine bases
Bioremediation 2006 March 17
Park Joonhong (C)
OBase
O- P
Creation of a DNA polynuleotide
through a phosphodiester bonds
linking the 3 and 5 carbons
of the deoxyribose units.
O
O
H
5
CH2
C 4
H
3
O
C 1
H
C
H
C 2
O
H
Base
O- P
Synthesis of
a DNA polynucleotide
O
O
H
5
CH2
O
C 4
H
3
Bioremediation 2006 March 17
Park Joonhong (C)
C 1
H
C
H
C 2
OH
H
DNA in a cell is in a double stranded form
Chromosome
Contain essential genes
Vertical transfer of DNA
Prokaryotic chromosome is circular, ds DNA
Prokaryotic chromosome 2 ~11 x106 base pairs
Archaea have 2 Mbps
Q: Eukryotic chromosome’s characteristics?
(Refer to p.85-86 in the main textbook)
B-form of ds DNA
c.f.) Z-form
Strand 1
5’
3’
Strand 2
3’
5’
Plasmid
Contain less essential genes
But contains environmentally important genes
(biodegradation, antibiotic resistance, metal reduction)
Horizontal transfer of DNA via conjugation,
transformation or virus transduction
Prokaryotic chromosome is usually circular, ds DNA
Shorter than chromosome but the length widely
varies from 0.1 Mbps to couple Mpbs.
Bioremediation 2006 March 17

Number
of plasmid can be none, one or more…
Park Joonhong (C)
DNA Replication
Critical Steps in DNA Replication
Separted in a region (origion); Replication fork
A DNA polymerase binds to one strand in the fork, and
moves from base to base along both strands in the 3’ to 5’
direction.
Generation of a complementary strand of DNA by the
polymerase (linking the deoxyribonucleoside triphosphate
complementary to the base at which the polymerase is
stationed to the previous base on the new, growing chain.
(leaning strand, lagged strand)
Termination of replication
 Exonuclease that detects errors, excises the incorrect
base, and replaces it with the correct one.
Bioremediation 2006 March 17
Park Joonhong (C)
Ribonucleic Acid (RNA)
B ase
OH
5
HOCH2
H
O
Hydrogen bond
H
O
C 4
H
3
Uracil (U)
C
NH
C 1
H
H
C 2
H
N
H
H
O
Base
Single stranded form (less
stable than dsDNA)
Messanger RNA (mRNA)
Ribose
unitunit
c.f.)
Ribose
Ribosomal RNA (rRNA)
Bioremediation 2006
March 17
Transfer
RNA (tRNA)
Park Joonhong (C)
OH
OH
Transcription: Conversion of DNA into RNA
DNA (Chromosome or plasmid)
Promotor
region
rRNA (16S, 32S –
forms ribosome,
“protein factory”)
Protein coding genes
mRNA
(translated into protein)
“Junk” DNA
(profound function)
tRNA
(shuttles for
amino acid)
Protein coding region in DNA => mRNA coding (open reading frame [ORF])
Non-protein coding region in DNA => rRNA coding, tRNA coding
Non-coding region in DNA => “Junk” DNA
Bioremediation 2006 March 17
Park Joonhong (C)
Transcription: Conversion of DNA into RNA
Critical Steps in Transcription
A RNA polymerase binds to a promoter region (typically 35 bases
ahead of where transcription begins)
The dsDNA separates, and the RNA polymerase moves from base
to base along one strand in its 3’ to 5’ direction.
Termination of transcription: stop at the end of gene; RNA
polymerase released from the DNA.
Gene Expression and Regulation
A RNA polymerase binds to a promoter region and produces mRNA
=> Gene Expression
Up-regulation (Expression): the synthesis of a mRNA is increased
Down-regulation (Repression): the synthesis of mRNA is reduced.
Inducible versus Constitute Expression
Regulation of a gene expression is highly influenced by
environmental and physiological
factors…(Why genomics is needed.)
Bioremediation 2006 March 17
Park Joonhong (C)
Translation: Conversion of mRNA into Protein
Translation by the
ribosome, containing
rRNA (large and
small subunits)
mRNA
Protein synthesis
Amino acid – tRNA
Bioremediation 2006 March 17
Park Joonhong (C)
Nucleotide Sequence of a Gene
1 atgagttcag caatcaaaga agtgcaggga gcccctgtga agtgggttac caattggacg
61 ccggaggcga tccgggggtt ggtcgatcag gaaaaagggc tgcttgatcc acgcatctac
121 gccgatcaga gtctttatga gctggagctt gagcgggttt ttggtcgctc ttggctgtta
181 cttgggcacg agagtcatgt gcctgaaacc ggggacttcc tggccactta catgggcgaa
241 gatccggtgg ttatggtgcg acagaaagac aagagcatca aggtgttcct gaaccagtgc
301 cggcaccgcg gcatgcgtat ctgccgctcg gacgccggca acgccaaggc tttcacctgc
361 agctatcacg gctgggccta cgacatcgcc ggcaagctgg tgaacgtgcc gttcgagaag
421 gaagcctttt gcgacaagaa agaaggcgac tgcggctttg acaaggccga atggggcccg
481 ctccaggcac gcgtggcaac ctacaagggc ctggtctttg ccaactggga tgtgcaggcg
541 ccagacctgg agacctacct cggtgacgcc cgcccctata tggacgtcat gctggatcgc
601 acgccggccg ggactgtggc catcggcggc atgcagaagt gggtgattcc gtgcaactgg
661 aagtttgccg ccgagcagtt ctgcagtgac atgtaccacg ccggcaccac gacgcacctg
721 tccggcatcc tggcgggcat tccgccggaa atggacctct cccaggcgca gatacccacc
781 aagggcaatc agttccgggc cgcttggggc gggcacggct cgggctggta tgtcgacgag
841 ccgggctcac tcctggcggt gatgggcccc aaggtcaccc agtactggac cgagggtccg
901 gctgccgagc ttgcggaaca gcgcctgggg cacaccggca tgccggttcg acgcatggtc
961 ggccagcaca tgacgatctt cccgacctgt tcattcctgc ccaccttcaa caacatccgg
1021 atctggcacc cgcgtggtcc caatgaaatc gaggtgtggg ccttcaccct ggtcgatgcc
1081 gacgccccgg cggagatcaa ggaagaatat cgccggcaca acatccgcaa cttctccgca
1141 ggcggcgtgt ttgagcagga cgatggcgag aactgggtgg agatccagaa ggggctacgt
1201 gggtacaagg ccaagagcca gccgctcaat gcccagatgg gcctgggtcg gtcgcagacc
1261 ggtcaccctg attttcctgg caacgtcggc tacgtctacg ccgaagaagc ggcgcggggt
1321 atgtatcacc actggatgcg catgatgtcc gagcccagct gggccacgct caagccctga
• bphA gene in Burkholderia xenovorans LB400
[gene index number:349602]
Bioremediation 2006 March 17
Park Joonhong (C)
Symbols for Amino Acids
A Ala alanine
R Arg Arginie
B Asx aspargine
S Ser Serine
C Cys Cysteine
T Thr Threonine
D Asp Aspartic acid
V Val Valine
E Glu Glutamic acid
W Trp Tryptophan
F Phe Phenylalanine
Y Tyr Tyrosine
G Gly Glycine
Z Glx Glutamine
H His Histidine
I Ile Isoleucine
K Lys Lysine
L Leu Leucine
M Met Methionine
N Asn Asparagine
P Pro Proline
Q Gln GlutamineBioremediation 2006 March 17
Park Joonhong (C)
Standard Genetic Code
UUU
UUC
UUA
UUG
Phe(F)
Phe(F)
Leu(L)
Leu (L)
UCU
UCC
UCA
UCG
Ser(S)
Ser(S)
Ser(S)
Ser(S)
UAU
UAC
UAA
UAG
Tyr (Y)
Tyr (Y)
Stop
Stop
UGU
UGC
UGA
UGG
Cys(C)
Cys(C)
Stop
Trp(W)
CUU
CUC
CUA
CUG
Leu (L)
Leu (L)
Leu (L)
Leu (L)
CCU
CCC
CCA
CCG
Pro(P)
Pro(P)
Pro (P)
Pro (P)
CAU
CAC
CAA
CAG
His (H)
His (H)
Gln(Q)
Gln(Q)
CGU
CGC
CGA
CGG
Arg (R)
Arg (R)
Arg (R)
Arg (R)
AUU
AUC
AUA
AUG
Ile (I)
Ile (I)
Ile (I)
Met(M)
ACU
ACC
ACA
ACG
Thr (T)
Thr (T)
Thr (T)
Thr (T)
AAU
AAC
AAA
AAG
Asn(N)
Asn(N)
Lys(K)
Lys(K)
AGU
AGC
AGA
AGG
Ser(S)
Ser(S)
Arg(R)
Arg(R)
GUU
GUC
GUA
GUG
Val(V)
Val (V)
Val (V)
Val (V)
GCU
GCC
GCA
GCG
Ala(A) GAU
Asp(D)
Ala(A) GAC
Asp(D)
Ala(A) GAA
Glu(E)
Bioremediation 2006 March 17
Ala(A)
GAG
Glu(E)
Park Joonhong
(C)
GGU
GGC
GGA
GGG
Gly(G)
Gly(G)
Gly(G)
Gly(G)
Amino Acid Sequence of a
Protein
Methods of obtaining amino acid sequences.
- Experimentally determined
- Bioinformatically translated using Standard Genetic Code
1 mssaikevqg apvkwvtnwt peairglvdq ekglldpriy adqslyelel ervfgrswll
61 lgheshvpet gdflatymge dpvvmvrqkd ksikvflnqc rhrgmricrs dagnakaftc
121 syhgwaydia gklvnvpfek eafcdkkegd cgfdkaewgp lqarvatykg lvfanwdvqa
181 pdletylgda rpymdvmldr tpagtvaigg mqkwvipcnw kfaaeqfcsd myhagttthl
241 sgilagippe mdlsqaqipt kgnqfraawg ghgsgwyvde pgsllavmgp kvtqywtegp
301 aaelaeqrlg htgmpvrrmv gqhmtifptc sflptfnnir iwhprgpnei evwaftlvda
361 dapaeikeey rrhnirnfsa ggvfeqddge nwveiqkglr gykaksqpln aqmglgrsqt
421 ghpdfpgnvg yvyaeeaarg myhhwmrmms epswatlkp
• BphA protein in Burkholderia xenovorans LB400
[gi:584852]
Bioremediation 2006 March 17
Park Joonhong (C)
Reading Assignments
For the Current Lecture
-Brock Biology of Microorganisms 12th; Ch.7