microbial ecology and environmental genomics

Microbial Ecology and Environmental Genomics

The 2nd Week

Introductions to

- Principles of Microbiology

- Molecular Biology of Microorganisms

Basics: Microbiology

• 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

The Cell (living entity)The Cell (living entity)


Eukaryotic cellEukaryotic cell Prokaryotic cellProkaryotic cell


• 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

Essential Cell ComponentsEssential Cell Components

Organism Classification

• Science of classification• Based upon observable properties (phenotypes) including

morphology and transformation• Traditional way of organism classification

TaxonomyTaxonomy

• Science of classification• Based upon evolution history (small subunit of rRNA,

functional gene sequencing, genome sequencing)• New way of organism classification

PhylogenyPhylogeny

• Escherichia coli O157:H7• Pseudomonas aeroginosa PA01• Burkholderia xenovorans LB400


Naming bacteria/archaeaNaming bacteria/archaea

RULE:RULE: Genus Genus (italic)(italic) species species (italic)(italic) strain strain(ref. the International Code of Nomenclature of Bacteria)(ref. the International Code of Nomenclature of Bacteria)

SpeciesSpecies: the basic taxonomic unit: the basic taxonomic unitGenusGenus: population unit: population unit


Membrane-enclosed nucleusMuramic acid in cell wallChlorophyll-based photosynthesisMethanogenesisReduction of S to H2SNitrificationDenitrificationNitrogen fixationSynthesis of poly-beta-hydroxylakanoate carbon storage granulesSensitivity to chloramphenicol, streptomycin, and kanamycinRebosome sensitivity to diphtheria toxin

Absent

Present

Yes

No

Yes

Yes

Yes

Yes

Yes

Yes

No

Absent

Absent

No

Yes

Yes

No

Yes

Yes

Yes

No

Yes

Present

Absent

Yes

No

No

No

No

No

No

No

Yes

BacteriaBacteria ArchaeaArchaea EukaryaEukaryaCharacteristicCharacteristic

Source: Madigan, Martinko, and Parker, 1997

Phylogenetic tree of life as determined from small subunit of ribosomal RNA sequencing (C. R. Woese)

-4.0

-3.0

-2.0

-1.0

-0.1

Origin of Earth (4.5 billion years)

Bacteria Eucarya Archaea

3.8Last common ancestorChemical evolution/Prebiotic synthesis of biomolecules

2.3

G+ Proteo- Cyano-

HGT

HGT

PlantMouse

Fruit fly

Origin of oxygenicphotosynthesis

Amito-chondriate

2.1

1.5

1.0

Crenarchaeota

Euryachaeota


• 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

Environmentally important microorganismsEnvironmentally important microorganisms

Prokaryotes

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

BacteriaBacteria

Archaea (laterArchaea (later……))

Bacteria

Coccus (spherical shape)

Streptococci

Staphylococci

Sarcina (packets of eight)

Bacillus (cylindrical rod shape)

Chains of bacilli

Spirillum (helical shape)

MorphologyMorphology

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

Size and some number for bacteriaSize and some number for bacteria

Bacteria

Cell wall: peptidoglycan (G-negatives have a higher content of lipopolysaccharide while G-positives teichoic acids)Cytoplasmic membrane: phospholipid bilayer, semipermeable, membrane-bound electron-transport enzymes (cytochromes), selective material transportCytoplasm: 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, rRNAEndospores (e.g. Bacillus, stress response)Capsule or slime layer: floc formationFlagella: chemotaxis, phototaxisFimbriae and pili: attachment, involved in conjugation

Cell structureCell structure

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

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

Chemical compositionChemical compositionMacromolecular compositionMacromolecular composition

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

molybdenum (N2 fixation)nickel (anaerobic methane production)cupper (methane oxidization)

Trace heavy metals in enzymesTrace heavy metals in enzymes

Bacteria (why C5H7O2N?)

Prokaryotic Reproduction

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 reproductionReplication: chromosome (genomic DNA) is replicated and divided into each daughter cell.

Replication ofchromosome

Norcardia species produce extensive filamentous growthFormation of long, branching, non-dividing filaments, containing multiple chromosomes. (Multi-cellular???)In stressed conditions, some of these species form spores (some Streptomyces and many molds)

Binary fission (normal way of multiplication)Binary fission (normal way of multiplication)

Filamentous growthFilamentous growth

Prokaryotic Reproduction

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.

Budding divisionBudding division

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).

Sexual reproduction via conjugationSexual reproduction via conjugation

Binary fission

Conjugation

Prokaryotic Growth Prokaryotic growth curveProkaryotic growth curve Calculation of growth rateCalculation of growth rate

The value of growth rate possibly is influenced by the way of quantifying growth (i.e., cell number counts vs. biomass).

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

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)

Energy and carbon-source classes of bacteriaEnergy and carbon-source classes of bacteria

Bacteria

• TemperaturePsychrophile (-5 to 20oC)

Mesophile (8 to 45 oC);

Thermophile (40 to 70oC)

Hyperthermophile (65 to 110 oC)

• pHTypically, 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.)

• OxygenAerobes (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)

• SaltsHalophiles (grow best under salt conditions

similar to seawater, 3.5% NaCl)

Extremehalophiles (live well in a saturated NaCl, 15-30%)

Environmental conditions for growthEnvironmental conditions for growth

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

Characteristics of 12 phylogenic lineages of bacteriaCharacteristics of 12 phylogenic lineages of bacteria

Proteobacteria (purple bacteria)

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

Major grouping of proteobacteriaMajor grouping of proteobacteria

* Phototrophic representatives (SOURCE: Madigan, Martinko, and Parker, 1997)

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

Pseudomonads (belonging to Pseudomonads (belonging to αα,,ββ, and, andγγ groups) groups)

Oxygen and

nitrateS

ulfate

TEA

AM

D,

Co

rro

sio

n

Archaea

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

Meaning of studying Archaea in BiotechnolgyMeaning of studying Archaea in Biotechnolgy

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.

Archaea versus BacteriaArchaea versus Bacteria

Archaea

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

Major groups and subgroupsMajor groups and subgroups

Eukarya

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

Of interest in environmental biotechnologyOf interest in environmental biotechnology

Viruses

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.)

Major characteristicsMajor characteristics

Infectious DiseasesMicroorganism

Class Group Organism name

Disease and symptoms

Virus

Bacteria

(Proteobacteria)

Algae

Protozoa

Viscerotropic

Viscerotropic

Neurotrophic

Epsilon

Epsilon

Gamma

Gamma

Gamma

Gamma

Gamma

Dinoflagellate

Dinoflagellate

Dinoflagellate

Mastigophora

Sarcodina

Sporozoa

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

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

Bioremediation 2006 March 17 Park Joonhong (C)

Ecosystem

Communities

Populations (at Genus level)

Cellular level

Subcellular level

gene (DNA) => mRNA => protein => enzyme =>function

rRNA

tRNA

Overview of Biology Systems


Information flow from the gene to the working enzyme catalyst

Deoxyribonucleic acid (DNA)(Chromosome, plasmid)

A gene

Replication

Messenger RNA(ribonucleic acids)

Transcription

Translation by the ribosome, containing ribosomal RNA

Protein enzyme

Amino acid – transfer RNA


Unit component of nucleic acids

C

O

C

C C

HOCH 2

HH H

H

OHOH

5

4

32

1

BaseOH

c.f.) Ribose unit

C

O

C

C C

HOCH 2

HH H

H

OHOH

5

4

32

1

BaseOH

c.f.) Ribose unit

H

Ribose unitRibose unit Deoxyribose unitDeoxyribose unit


Deoxynucleotide unit

C

O

C

C C

CH2

HH H

H

HOH

5

4

32

1

Monophosphate deoxynucleotide

OP

O-

O

O-

Ester bond formed with release of H2O

Base

Deoxyribose

Glycosidic bondformed with releaseof H2O.


N

N

H

H

N

N

NH2

H

N

N

H

H

N

NH

O

NH2

N

H

NH

H

H3C

OAdenine (A)

Guanine (G)

Thymine

N

H

NH

H

H

NH2Cytosine (C)

O

PurinePurine basesPurine bases Pyrimidine basesPyrimidine bases

H

HH

Hydrogen bond

O

Hydrogen bond

A-T compliment bondA-T compliment bond

G-C compliment bondG-C compliment bond


C

O

C

C C

CH2

HH H

H

HOH

5

4

32

1

OP

O

O

O-

Base

C

O

C

C C

CH2

HH H

H

H

5

4

32

1

OP

O-

O

O-

Base

Creation of a DNA polynuleotide through a phosphodiester bondslinking the 3 and 5 carbonsof the deoxyribose units.

Synthesis of Synthesis of a DNA polynucleotide a DNA polynucleotide


DNA in a cell is in a double stranded form

B-form of ds DNAB-form of ds DNAc.f.) Z-formc.f.) Z-form

Contain essential genesVertical transfer of DNA Prokaryotic chromosome is circular, ds DNAProkaryotic chromosome 2 ~11 x106 base pairsArchaea have 2 MbpsQ: Eukryotic chromosome’s characteristics? (Refer to p.85-86 in the main textbook)

Contain less essential genesBut 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 DNAShorter than chromosome but the length widely varies from 0.1 Mbps to couple Mpbs. Number of plasmid can be none, one or more…

ChromosomeChromosome

PlasmidPlasmid

Strand 1 Strand 2

5’

5’

3’

3’


DNA Replication

Separted in a region (origion); Replication forkA 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.

Critical Steps in DNA ReplicationCritical Steps in DNA Replication


Ribonucleic Acid (RNA)

C

O

C

C C

HOCH 2

HH H

H

OHOH

5

4

32

1

BaseOH

c.f.) Ribose unitRibose unitRibose unit

N

H

NH

H

H

OUracil (U)

H

Hydrogen bond

O

BaseBase

Single stranded form (less stable than dsDNA)Messanger RNA (mRNA)Ribosomal RNA (rRNA)Transfer RNA (tRNA)


Transcription: Conversion of DNA into RNA

DNA (Chromosome or plasmid)

rRNA (16S, 32S – forms ribosome, “protein factory”)

mRNA (translated into protein)

Protein coding genes

tRNA(shuttles for amino acid)

Promotorregion

“Junk” DNA (profound function)

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


Transcription: Conversion of DNA into RNA

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.

Critical Steps in TranscriptionCritical Steps in Transcription

A RNA polymerase binds to a promoter region and produces mRNA => Gene Expression Up-regulation (Expression): the synthesis of a mRNA is increasedDown-regulation (Repression): the synthesis of mRNA is reduced.Inducible versus Constitute ExpressionRegulation of a gene expression is highly influenced by environmental and physiological factors…(Why genomics is needed.)

Gene Expression and RegulationGene Expression and Regulation


Translation: Conversion of mRNA into Protein

mRNA

Translation by the ribosome, containing rRNA (large and small subunits)

Amino acid – tRNA

Protein synthesis


Nucleotide Sequence of a Gene1 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]


Symbols for Amino AcidsA Ala alanineB Asx aspargineC Cys CysteineD Asp Aspartic acidE Glu Glutamic acidF Phe PhenylalanineG Gly GlycineH His HistidineI Ile IsoleucineK Lys LysineL Leu LeucineM Met MethionineN Asn AsparagineP Pro ProlineQ Gln Glutamine

R Arg ArginieS Ser SerineT Thr ThreonineV Val ValineW Trp TryptophanY Tyr TyrosineZ Glx Glutamine


Standard Genetic CodeUUU

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)

Ala(A)

Ala(A)

Ala(A)

GAU

GAC

GAA

GAG

Asp(D)

Asp(D)

Glu(E)

Glu(E)

GGU

GGC

GGA

GGG

Gly(G)

Gly(G)

Gly(G)

Gly(G)


Amino Acid Sequence of a Protein

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]

Methods of obtaining amino acid sequences.- Experimentally determined- Bioinformatically translated using Standard Genetic Code

Reading Assignments

For the Current Lecture -Brock Biology of Microorganisms 12th; Ch.7

microbial ecology and environmental genomics

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