1. The study characterized the excreted proteome of Enterococcus faecalis and found it is regulated temporally by the Fsr quorum sensing system, with GelE post-translationally regulating the proteome.
2. A protein called SalB was found to be constitutively expressed in a gelE mutant. Deletion of salB caused stress responses and changes to the excreted protein profile.
3. SalB has peptidoglycan hydrolase activity but its specificity is unknown. The salB deletion mutant showed cell morphological defects including septation anomalies.
Evaluation of the lacZ gene in Escherichia coli mutagenesis using pBluescript...Emilio Solomon
This was a research paper I wrote for my Integrated Laboratory Techniques in Biological Sciences II course.
Evaluation of the lacZ gene in Escherichia coli mutagenesis using pBluescript and pTn5: Km vectors
Enzyme Discovery for Natural Product BiosynthesisHongnan Cao
A poster presentation of collaborative work on the NIH funded project of Enzyme Discovery for Natural Product Biosynthesis at 2015 American Crystallography Association Meeting at Philadelphia, PA. Thanks to Rice University, University of Wisconsin-Madison, The Scripps Research Institute, University of Kentucky, The Midwest Center for Structural Genomics, The Northeast Center for Structural Genomics, APS synchrotron at Argonne National Lab
Evaluation of the lacZ gene in Escherichia coli mutagenesis using pBluescript...Emilio Solomon
This was a research paper I wrote for my Integrated Laboratory Techniques in Biological Sciences II course.
Evaluation of the lacZ gene in Escherichia coli mutagenesis using pBluescript and pTn5: Km vectors
Enzyme Discovery for Natural Product BiosynthesisHongnan Cao
A poster presentation of collaborative work on the NIH funded project of Enzyme Discovery for Natural Product Biosynthesis at 2015 American Crystallography Association Meeting at Philadelphia, PA. Thanks to Rice University, University of Wisconsin-Madison, The Scripps Research Institute, University of Kentucky, The Midwest Center for Structural Genomics, The Northeast Center for Structural Genomics, APS synchrotron at Argonne National Lab
Comparative evaluation of antimicrobial efficacy of q mix™/ dental implant co...Indian dental academy
The Indian Dental Academy is the Leader in continuing dental education , training dentists in all aspects of dentistry and
offering a wide range of dental certified courses in different formats.
Comparative evaluation of antimicrobial efficacy of q mix™/ dental implant co...Indian dental academy
The Indian Dental Academy is the Leader in continuing dental education , training dentists in all aspects of dentistry and
offering a wide range of dental certified courses in different formats.
Research by Mahendra Trivedi - Impact of an external energy on Enterococcus f...Abby Keif
Research on Trivedi Effect - The present experiments on Enterococcus faecalis [ATCC –51299], report the effects of biofield energy transmitted through a person, Mr. Mahendra Kumar Trivedi, which has produced an impact measurable in scientifically rigorous manner.
Antimicrobial activity of annona muricata L. (Soursop Leaves)Fattah Fazel
Testing antimicrobial activity of Annona Muricata L. (Soursop) using Disk diffusion method and Well diffusion method.
Bacteria used: MRSA, S.pyogenes, B. fragilis, C. perfringens
Note: No results. Reasons in the description section.
Lab: Differential Expression Differential gene expression provides the ability for a cell or
organism to respond to a constantly changing external environment. The specific constellation of
proteins required for optimal function and growth varies with cellular age and environmental
context. Thus, protein production is carefully regulated by multiple mechanisms that modulate
both transcriptional and translational pathways. Control of transcription initiation by RNA
polymerase is a predominant mechanism for regulating expression of specific proteins,
presumably because it provides maximal conservation of energy for the cell. We can often
observe the consequence of differential transcription due to the presence or absence of particular
proteins or the growth in particular environments. Control can also occur at translation; the
mRNA is synthesized, but only in certain circumstances is it translated. Control can also occur at
the level of protein function; the protein is inactive, or activity is not observed due to the lack of
the substrate. In this lab we will observe differential expression of two different genes encoded
on plasmids. We will analyze transcriptional activity, translational activity, and protein function.
Plasmids are extra-chromosomal DNA. Bacteria often have plasmids and will replicate the
plasmid and pass it to daughter cells (vertical transmission) and to neighboring cells (horizontal).
Plasmids are a mechanism of gene diversity. In order to stably retain the plasmid, there needs to
be some type of metabolic reason for the bacteria to maintain the plasmid. In other words, the
plasmid confers an advantage. Plasmids contain: 1. Ori: the plasmid may present is low or high
copy number. 2. Lab generated plasmids typically also contain a selectable marker (antibiotic
resistance), 3. Additional gene for ease of visual screening 4. Multiple cloning site
pUC19 is one of a series of plasmid cloning vectors created by Joachim Messing and co-workers.
The designation "pUC" is derived from the classical "p" prefix (denoting "plasmid") and the
abbreviation for the University of California, where early work on the plasmid series had been
conducted. It is a circular double stranded DNA and has 2686 base pairs. pUC19 is one of the
most widely used vector molecules as the recombinants, or the cells into which foreign DNA has
been introduced, can be easily distinguished from the non-recombinants based on color
differences of colonies on growth media. pUC18 is similar to pUC19, but the MCS region is
reversed. - pUC 19 has an origin of replication and is maintained at a high copy number. -
pUC19 encodes for an ampicillin resistance gene (amopR), via a -lactamase enzyme that
functions by degrading ampicillin and reducing its toxicity to the host. - It has an N-terminal
fragment of -galactosidase (lacZ) gene of E. coli which allows for visual screening of
recombinant plasmids. The transformed cells containing the plasmid with the gene of interest ca.
Lab: Differential Expression Differential gene expression provides the ability for a cell or
organism to respond to a constantly changing external environment. The specific constellation of
proteins required for optimal function and growth varies with cellular age and environmental
context. Thus, protein production is carefully regulated by multiple mechanisms that modulate
both transcriptional and translational pathways. Control of transcription initiation by RNA
polymerase is a predominant mechanism for regulating expression of specific proteins,
presumably because it provides maximal conservation of energy for the cell. We can often
observe the consequence of differential transcription due to the presence or absence of particular
proteins or the growth in particular environments. Control can also occur at translation; the
mRNA is synthesized, but only in certain circumstances is it translated. Control can also occur at
the level of protein function; the protein is inactive, or activity is not observed due to the lack of
the substrate. In this lab we will observe differential expression of two different genes encoded
on plasmids. We will analyze transcriptional activity, translational activity, and protein function.
Plasmids are extra-chromosomal DNA. Bacteria often have plasmids and will replicate the
plasmid and pass it to daughter cells (vertical transmission) and to neighboring cells (horizontal).
Plasmids are a mechanism of gene diversity. In order to stably retain the plasmid, there needs to
be some type of metabolic reason for the bacteria to maintain the plasmid. In other words, the
plasmid confers an advantage. Plasmids contain: 1. Ori: the plasmid may present is low or high
copy number. 2. Lab generated plasmids typically also contain a selectable marker (antibiotic
resistance), 3. Additional gene for ease of visual screening 4. Multiple cloning site
pUC19 is one of a series of plasmid cloning vectors created by Joachim Messing and co-workers.
The designation "pUC" is derived from the classical "p" prefix (denoting "plasmid") and the
abbreviation for the University of California, where early work on the plasmid series had been
conducted. It is a circular double stranded DNA and has 2686 base pairs. pUC19 is one of the
most widely used vector molecules as the recombinants, or the cells into which foreign DNA has
been introduced, can be easily distinguished from the non-recombinants based on color
differences of colonies on growth media. pUC18 is similar to pUC19, but the MCS region is
reversed. - pUC 19 has an origin of replication and is maintained at a high copy number. -
pUC19 encodes for an ampicillin resistance gene (amopR), via a -lactamase enzyme that
functions by degrading ampicillin and reducing its toxicity to the host. - It has an N-terminal
fragment of -galactosidase (lacZ) gene of E. coli which allows for visual screening of
recombinant plasmids. The transformed cells containing the plasmid with the gene of interest ca.
Regulation of gene expression in prokaryotes finalICHHA PURAK
The power point presentation explains about regulation of gene expression in prokaryotes by means of Inducible and repressible operons with the help of Lactose(lac) operon and Tryptophan (trp)
1 At least 2 questions from this section will be on the .docxmercysuttle
1
At least 2 questions from this section will be on the final exam
SAMPLE QUESTIONS FOR THE FINAL EXAM
Question 1. Ferritin is a protein involved in the storage of iron inside cells. To prevent toxic accumulation of
too much iron inside cells, the intracellular level of ferritin is tightly regulated. To study the regulation of
ferritin synthesis, mammalian cells are grown with or without iron in the culture medium. Note that iron in the
culture medium is rapidly transported inside cells.
a) Upon addition of iron to the culture medium, the intracellular concentration of ferritin mRNA is unchanged
but the concentration of ferritin protein increases. How do you think ferritin expression is regulated? Briefly
explain.
The regulatory sequence given below is found in the ferritin mRNA between the cap structure and the start
codon.
5’-GGGUUUCCGUUCAACAGUGCUUGGACGGAAACCC-3’
Mutations within in this sequence are used to study the regulation of ferritin expression. The following
observation are made:
• ferritin expression is high, independent of the iron concentration, when (i) the entire region is deleted, or
(ii) the region located upstream of the underlined sequence is deleted or (iii) the underlined sequence is
replaced with a random sequence.
• ferritin expression remains iron-dependent when this region is replaced by the following sequence:
5’-GGGCUCAGGUUCAACAGUGCUUGGACCUGAGCCC-3’.
Note that the sequence differences are indicated in bold.
b) Explain why these observations suggest that both sequence and structure of the 5’ end of ferritin mRNA are
important for the regulation of ferritin expression.
c) Ferritin translation becomes iron-independent when the regulatory sequence is moved from the 5’ side
(upstream of the open reading frame) to the 3’ side (downstream of the open reading frame) of ferritin mRNA.
Which step of ferritin translation do you think is affected by the intracellular level of iron?
d) IRP is a protein involved in the regulation of ferritin expression. Anti-IRP antibodies attached to sepharose
beads are added to a cell extract, then the extract is centrifuged to separate the pellet fraction (containing the
sepharose beads ) from the supernatant fraction.
If the cells are cultured in the absence of iron, ferritin mRNA is found together with IRP in the pellet. In
contrast when cells are cultured in the presence of iron ferritin mRNA remains in the supernatant fraction while
IRP alone is found in the pellet. Briefly explain the likely role of IRP in the regulation of ferritin expression.
Question 2. You are studying the development of a newly discovered insect. Like drosophila, it undergoes a
stage in early larval development where the eve gene is expressed in a pattern of 7 stripes. You are particularly
interested in stripes 2 and 5. The following figures show the organization of the cis-acting elements that control
the expression o ...
ONLY THE LAST QUESTION IS THE POINT OF POST. THE OTHER PAGES ARE B.pdfamzonknr
ONLY THE LAST QUESTION IS THE POINT OF POST. THE OTHER PAGES ARE
BACKGROUND CONTEXT Lab: Differential Expression Differential gene expression provides
the ability for a cell or organism to respond to a constantly changing external environment. The
specific constellation of proteins required for optimal function and growth varies with cellular
age and environmental context. Thus, protein production is carefully regulated by multiple
mechanisms that modulate both transcriptional and translational pathways. Control of
transcription initiation by RNA polymerase is a predominant mechanism for regulating
expression of specific proteins, presumably because it provides maximal conservation of energy
for the cell. We can often observe the consequence of differential transcription due to the
presence or absence of particular proteins or the growth in particular environments. Control can
also occur at translation; the mRNA is synthesized, but only in certain circumstances is it
translated. Control can also occur at the level of protein function; the protein is inactive, or
activity is not observed due to the lack of the substrate. In this lab we will observe differential
expression of two different genes encoded on plasmids. We will analyze transcriptional activity,
translational activity, and protein function. Plasmids are extra-chromosomal DNA. Bacteria often
have plasmids and will replicate the plasmid and pass it to daughter cells (vertical transmission)
and to neighboring cells (horizontal). Plasmids are a mechanism of gene diversity. In order to
stably retain the plasmid, there needs to be some type of metabolic reason for the bacteria to
maintain the plasmid. In other words, the plasmid confers an advantage. Plasmids contain: 1. Ori:
the plasmid may present is low or high copy number. 2. Lab generated plasmids typically also
contain a selectable marker (antibiotic resistance), 3. Additional gene for ease of visual screening
4. Multiple cloning site
pUC19 is one of a series of plasmid cloning vectors created by Joachim Messing and co-workers.
The designation "pUC" is derived from the classical "p" prefix (denoting "plasmid") and the
abbreviation for the University of California, where early work on the plasmid series had been
conducted. It is a circular double stranded DNA and has 2686 base pairs. pUC19 is one of the
most widely used vector molecules as the recombinants, or the cells into which foreign DNA has
been introduced, can be easily distinguished from the non-recombinants based on color
differences of colonies on growth media. pUC18 is similar to pUC19, but the MCS region is
reversed. - pUC 19 has an origin of replication and is maintained at a high copy number. -
pUC19 encodes for an ampicillin resistance gene (amopR), via a -lactamase enzyme that
functions by degrading ampicillin and reducing its toxicity to the host. - It has an N-terminal
fragment of -galactosidase (lacZ) gene of E. coli which allows for visual screening of
recombinant.
ONLY THE LAST QUESTION IS THE POINT OF POST. THE OTHER PAGES ARE BAC.pdfamzonknr
ONLY THE LAST QUESTION IS THE POINT OF POST. THE OTHER PAGES ARE
BACKGROUND CONTEXT Lab: Differential Expression Differential gene expression provides
the ability for a cell or organism to respond to a constantly changing external environment. The
specific constellation of proteins required for optimal function and growth varies with cellular
age and environmental context. Thus, protein production is carefully regulated by multiple
mechanisms that modulate both transcriptional and translational pathways. Control of
transcription initiation by RNA polymerase is a predominant mechanism for regulating
expression of specific proteins, presumably because it provides maximal conservation of energy
for the cell. We can often observe the consequence of differential transcription due to the
presence or absence of particular proteins or the growth in particular environments. Control can
also occur at translation; the mRNA is synthesized, but only in certain circumstances is it
translated. Control can also occur at the level of protein function; the protein is inactive, or
activity is not observed due to the lack of the substrate. In this lab we will observe differential
expression of two different genes encoded on plasmids. We will analyze transcriptional activity,
translational activity, and protein function. Plasmids are extra-chromosomal DNA. Bacteria often
have plasmids and will replicate the plasmid and pass it to daughter cells (vertical transmission)
and to neighboring cells (horizontal). Plasmids are a mechanism of gene diversity. In order to
stably retain the plasmid, there needs to be some type of metabolic reason for the bacteria to
maintain the plasmid. In other words, the plasmid confers an advantage. Plasmids contain: 1. Ori:
the plasmid may present is low or high copy number. 2. Lab generated plasmids typically also
contain a selectable marker (antibiotic resistance), 3. Additional gene for ease of visual screening
4. Multiple cloning site
pUC19 is one of a series of plasmid cloning vectors created by Joachim Messing and co-workers.
The designation "pUC" is derived from the classical "p" prefix (denoting "plasmid") and the
abbreviation for the University of California, where early work on the plasmid series had been
conducted. It is a circular double stranded DNA and has 2686 base pairs. pUC19 is one of the
most widely used vector molecules as the recombinants, or the cells into which foreign DNA has
been introduced, can be easily distinguished from the non-recombinants based on color
differences of colonies on growth media. pUC18 is similar to pUC19, but the MCS region is
reversed. - pUC 19 has an origin of replication and is maintained at a high copy number. -
pUC19 encodes for an ampicillin resistance gene (amopR), via a -lactamase enzyme that
functions by degrading ampicillin and reducing its toxicity to the host. - It has an N-terminal
fragment of -galactosidase (lacZ) gene of E. coli which allows for visual screening of
recombinant.
5. GelE Temporally Regulates the Excreted Protein profile, particularly SalB Temporal regulation of excreted proteins of E. faecalis OG1RF and its isogenic gelE and fsrB mutants separated on a 11% gel. Samples were collected at mid-log (3h), late-log (5h), stationary (8h) and overnight (ON) phases of growth. M = Biorad Broad range marker
6.
7. SalB is a Peptidoglycan Hydrolase with Unknown Specificity Left: Figure showing the separation of dilutions of purified SalB ( μ g) on a 11% gel stained with coomassie blue Right: Figure showing a 11% renaturing gel with 10 OD units of E. faecalis purified peptidoglycan stained with 0.1% methylene blue; Zones of clearing indicate SalB activity M=Page ruler, prestained marker
8. Functional analysis – HPLC for the identification of bond specificity Mutanolysin Mutanolysin + SalB Figure showing the HPLC separation of reduced mutanolysin or mutanolysin + SalB digested E. faecalis OG1RF peptidoglycan on a linear 0-45% gradient over 65 minutes
9.
10. Functional analysis – HPLC for the identification of bond specificity Mutanolysin treated OG1RF salB peptidoglycan Mutanolysin + heat treated SalB
16. SalB Deletion Results in a Hyper-Lytic Phenotype A B Fig 6: Autolysis assays for E. faecalis OG1RF ( ) and its isogenic mutants OG1RF gelE ( ), OG1RF fsrB ( ), OG1RF salB (▲), and double mutants OG1RF gelE/salB ( ) and OG1RF fsrB/salB ( ) conducted in 0.1mgml -1 Penicillin G ( A ) or 0.1% (v/v) Triton X-100 ( B ) induced stress. Exponentially growing cells were harvested, washed in PBS and resuspended in PBS containing 0.1mgml -1 Penicillin G or 0.1% v/v Triton X 100. Optical density at 600nm was collected hourly and turbidity was plotted as a percentage survival graph versus time.
17.
18.
19. With thanks to: Bacterial Pathogenesis Group: Dr. Mal Horsburgh Dr. John Kenny Ben Libberton Rachel Walker Proteomics: Dr. Deborah Ward Mark Prescott HPLC: Dr. Mark Wilkinson Confocal imaging and Flow Cytometry: Dr. Dave Spiller TEM: Allison Beckett Dr. Ian Prior And all members of LabH
Editor's Notes
HI IM Jay and Im here to talk about the characterisation of the E. faecalis excretome and in particular the role and regulation of SalB, a putative autolysin. Enterococci are medically relevant particularly due to their capability to transfer antibiotic resitance, including Vancomycin resistance to other, more pathogenic bacteria including Staphylococci.
Both cell wall associated and excreted virulence determinants of Enterococci are being characterised. The role of its physiology becomes important to better understanding this organism. The specific aims of the project was to characterise the excreted protein profile of E. faecalis OG1RF, a quorum sensing replete strain that produces a protease GelE, a known virulence agent.
We are concerned with the quorum sensing fsr Two component system that regulates the expression of proteases Gelatinase (GelE ) and serine protease (SprE) The current model described for the operon is the accumulation of GBAP (gelatinase biosynthesis activating pheromone), which is an autoinducing peptide. The product of fsrD gene is detected by cell wall associated FsrC (Histidine kinase) which phosphosphorylates FsrA (Response regulator) which in turn regulates gene expression, particularly GelE and SprE, but also other genes. GelE, is involved in increasing autolysis, reduces aggregation and degrades polymerised fibrin. Its contribution to virulence has been established in animal models.
2D analysis of stationary phase proteins revealed a dominance of GelE and SprE. A total of 54 spots were excised and 44 were ascribed identifications based on matches to the MASCOT database of tryptic fragments of excised protein spots analysed by MALDI-TOF. The red arrows indicate proteins that we were unable to identify. Few obvious potential virulence determinants, sulphatase domain protein may aid in colonisation of mucosal surfaces, but most others are concerned with cell wall biosynthesis and stress response.
Note: Temporal regulation due to protease activity(?) in OG1RF To study the effect of GelE on the regulation of excreted proteins of OG1RF, excreted proteins from the wildtype, a gelE mutant and and fsrB mutant were compared. Where the wildtype expresses a shift in profile into stationary phase, the mutants lacking GelE do not show this shift. Among the bands constitutively expressed, SalB was identified by Rachel Walker.
And that was how we got interested in SalB. Previously, work has been published on SalB. It was recognised as a stress related protein, potentially conferring stress relief as it was identified on 2-D gels of proteins differentially expressed in E. faecalis JH2-2 (an fsr lacking strain) that were stressed by bile salt and glucose starvation when compared to the wild type. It was also identified by an American group as a homolouge of SagA of E. faecium (which binds ECM molecules and contributes to virulence) and studies indicate that SalB performs similar function in E. faecalis, potentially contributing to virulence The Deletion of SalB in JH22 was also noted to cause severe growth defects and morphological changes, particularly sepatation anamolies as studied by TEM. These authors suggest a role of SalB in stress relief by some cell wall modification process.
Purified SalB was applied to an SDSPAGE gel with 10-OD units worth of E. faecalis peptidoglycan. Following separation, the proteins were renatured with triton and Mg2+ and the peptidoglycan was stained with Methylene blue. Zones of clearing indicate activity of SalB on the PG. Explain figure
Purified peptidoglycan was digested with mutanolysin (a muramidase) and mutanolysin with SalB overnight. Digested muropeptides were reduced in the presence of Sodium borohydride and separated by HPLC over 65 minutes on a 45% linear gradient As is evident (picture) additional peaks were seen on the mutanolysin + salB fraction, and these were assumed to be as a result of SalB action
Masses were calculated from monomers and dimers as a possible result for muramidase and endopeptidase activity. The unique fractions were collected and analysed by MS, however, we only identified SalB fragments. Before we got ahead of ourselves assuming that it was PG binding regions, we decided to make sure that it was not fractions of SalB from degradation. The following experiments were designed and conducted (from slide) However, Heat treated SalB also produced the same effect indicating that these peaks were probably SalB degrading overnight in the presence of Mutanolysin. (as confirmed by SDS-PAGE). At this point, no direct action on PG could be assigned to SalB
As represented here, we were unable to pick up any peptidoglycan modification caused by the deletion of the salB gene in the mutant. Also the heat treatment of SalB overexpressed protein continued to produe a profile similar to un-heated sample indicating that the additional peaks observed were probably not due to SalB activity on peptidoglycan
To characterise the effect of SalB on the physiology of E. faecalis, SalB deletions were constructed in E. faecalis OG1RF and also in the gelE and fsrB mutants. Additionally, sal B was complemented in the knockout strain.
2D DIGE was performed. Flouro labelled proteins from OG1RF and OG1RF salB were applied to the same gel. After separation, they were excited at appropriate wavelengths and images were overlaid.
The effect of SalB on protein expression was analysed by 2D SDSPAGE 32 spots differentially expressed in the mutant compared to the wildtype. 32 spots were excised and 25 were identified. Red arrows indicate spots we were unable to ascribe an id to OF interest are spots A, C, F and V which are related to stress management. The cell seems to be induced into a stressed state when SalB activity is removed. However, our method for growth includes shaking which introduces O2 stress.
Morphologies of the various strains were analysed by LSM under 100x after the cells were stained with BACLIGHT live dead kit from invitrogen. Greeen cells are live and red cells are dead. A chaining phenotype is seen in the fsrB and gelE deletions. This has been described before. However, a “clumping” phenotype is observed in the SalB deletion mutant. The double mutant shows an exacerbated condition of clumping and chaining. Note the varying scale bars.
Additionally septum formation was studied using TEM. Again, SalB deletion in the wildtype or the OG1RF gelE background show abnormal septum formation and the condition is exacerbated in the double mutant.
In induced autolysis experiments using cell wall active Penicillin G and surfactant triton , salB deletion causes the cell to show increased lysis either in the wildtype or the GelE mutant. IN both cases, the deletion of salB leads to increased susceptibility to PenG and triton. However, the GelE mutant exhibits a classical autolysin deficient response – increased susceptibility.