Genome of the week - Enterococcus faecalis

1
Genome of the week - Enterococcus faecalis

• E. faecalis - urinary tract infections,
  bacteremia, endocarditis.
• Organism sequenced is vancomycin resistant.
• Vancomycin is often last available antibiotic -
  resistance to this drug often means no other
  antibiotics will work.
• Major cause of nosocomial infections.
• Possible transfer of vanomycin resistance genes
  to more serious pathogens is a major concern.

2
Genome of the week - Enterococcus faecalis

• Over 25 of the E. faecalis genome consists of
  foreign DNA.
• Phages, insertions sequences, transposons.
• Likely contributed to the acquisition of
  resistance to multiple antibiotics.
• Over 35 PTS systems
• Responsible for transporting sugars into the
  cell.
• Most found in any sequenced genome, likely
  utilize undigested sugars in the intestine.

3
The omics nomenclature
4
Why study protein expression?
5

• 2D gel electrophoresis
• Method for separating and visualizing proteins
• Separation by charge and mass
• Mass spectrometry
• High throughput analysis and identification of
  proteins.
• Fragmentation of proteins
• Analysis of peptides
• Book - pages 273-300.

6
2D-SDS PAGE gel
The first dimension (separation by isoelectric
focusing) - gel with an immobilised pH gradient -
electric current causes charged proteins to move
until it reaches the isoelectric point (pH
gradient makes the net charge 0) What determines
the charge of a protein?
7
Isoelectric point (pI)

• Separation by charge

Low pH Protein is positively charged
At the isolectric point the protein has no net
charge and therefore no longer migrates in the
electric field.
High pH protein is negatively charged
8
2D-SDS PAGE gel
The first dimension (separation by isoelectric
focusing) - gel with an immobilised pH gradient -
electric current causes charged proteins to move
until it reaches the isoelectric point (pH
gradient makes the net charge 0)
The second dimension (separation by mass) -pH
gel strip is loaded onto a SDS gel -SDS denatures
the protein (to make movement solely dependent on
mass, not shape) and eliminates charge.
9
2D-SDS PAGE gel
10
2D-gel technique example
11
Advantages vs. Disadvantages

• Not for hydrophobic proteins
• Limited by pH range
• Not easy for low abundant proteins
• Analysis and quantification are difficult

• Good resolution of proteins
• Detection of posttranslational modifications

12
Current Mass Spec Technologies

• Proteome profiling/separation
• 2D SDS PAGE - identify proteins
• 2-D LC/LC - high throughput analysis of lysates
• (LC Liquid Chromatography)
• 2-D LC/MS
• (MS Mass spectrometry)
• Protein identification
• Peptide mass fingerprint
• Tandem Mass Spectrometry (MS/MS)
• Quantative proteomics
• ICAT (isotope-coded affinity tag)
• ITRAQ

13
Mass Spectrometry (MS)

• Introduce sample to the instrument
• Generate ions in the gas phase
• Separate ions on the basis of differences in m/z
  with a mass analyzer
• Detect ions

14
2D - LC/LC
Peptides all bind to cation exchange column
(trypsin)
Study protein complexes without gel
electrophoresis
Successive elution with increasing salt gradients
separates peptides by charge
Peptides are separated by hydrophobicity on
reverse phase column
Complex mixture is simplified prior to MS/MS by
2D LC
15
2D - LC/MS
16
Methods for protein identification
17
Identifying proteins

• Trypsin - digest your protein
• Digests after R and K amino acids.
• Run peptide fragments on mass spec
• Digest the protein database in silico
• Compare mass spec data with theoretical data.
• What must be true to identify your protein?

18
Protein Identification by MS
Spectrum of fragments generated
MATCH
Library
Database of sequences (i.e. SwissProt)
19
How protein sequencing works

• Use Tandem MS two mass analyzer in series with a
  collision cell in between
• Collision cell a region where the ions collide
  with a gas (He, Ne, Ar) resulting in
  fragmentation of the ion
• Fragmentation of the peptides in the collision
  cell occur in a predictable fashion, mainly at
  the peptide bonds
• The resulting daughter ions have masses that are
  consistent with known molecular weights of
  dipeptides, tripeptides, tetrapeptides

Ser-Glu-Leu-Ile-Arg-Trp
Collision Cell
Ser-Glu-Leu-Ile-Arg
Ser-Glu-Leu-Ile
Ser-Glu-Leu
Etc
20
(No Transcript)
21
Advantages vs. Disadvantages

• High capital costs
• Requires sequence databases for analysis

• Determination of MW and aa. Sequence
• Detection of posttranslational modifications
• High-throughput capability

22
ISOTOPE-CODED AFFINITY TAG (ICAT) a quantitative
method

• Label protein samples with heavy and light
  reagent
• Reagent contains affinity tag and heavy or light
  isotopes

Chemically reactive group forms a covalent bond
to the protein or peptide
Isotope-labeled linker heavy or light, depending
on which isotope is used
Affinity tag enables the protein or peptide
bearing an ICAT to be isolated by affinity
chromatography in a single step
23
Example of an ICAT Reagent
Biotin Affinity tag Binds tightly to
streptavidin-agarose resin
Reactive group Thiol-reactive group will bind to
Cys
Linker Heavy version will have deuteriums at
Light version will have hydrogens at
24
How ICAT works?
Affinity isolation on streptavidin beads
Lyse Label
Quantification MS
Identification MS/MS
NH2-EACDPLR-COOH
Light
100
MIX
Heavy
Proteolysis (eg trypsin)
m/z
m/z
25
Advantages vs. Disadvantages

• Estimates relative protein levels between samples
  with a reasonable level of accuracy (within 10)
• Can be used on complex mixtures of proteins
• Cys-specific label reduces sample complexity
• Peptides can be sequenced directly if tandem
  MS-MS is used

• Yield and non specificity
• Slight chromatography differences
• Expensive
• Tag fragmentation
• Meaning of relative quantification information
• No presence of cysteine residues or not
  accessible by ICAT reagent