Alex A. Cardenas Week 11: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
Line 2: Line 2:
*Working with both Zeb and Bobby for the final project.
*Working with both Zeb and Bobby for the final project.
*We are looking at and research Staphylococcus aureus.
*We are looking at and research Staphylococcus aureus.
**The microarray we will be using is on this [[http://www.ebi.ac.uk/arrayexpress/experiments/E-BUGS-65 article]].
**The microarray data we will be using is on this article. [[http://www.ebi.ac.uk/arrayexpress/experiments/E-BUGS-65 Found here]].
**Microarray data article[[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123200/?tool=pubmed here]].
**Microarray data article can be found [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123200/?tool=pubmed here]].


=Article Outline=
=Article Outline=

Revision as of 17:46, 9 November 2011

Final Presentation

  • Working with both Zeb and Bobby for the final project.
  • We are looking at and research Staphylococcus aureus.
    • The microarray data we will be using is on this article. [Found here].
    • Microarray data article can be found [here].

Article Outline

Abstract

  • Background
    • Staphylococcus aureus - human pathogen. Treatments are needed. Antimicrobial peptides potential antibiotic to MRSA.
      • Such as Renalexin - fights against gram positive bacteria, S. aureus in particular.
    • Study of drug resistance and mode of action is important.
  • Results
    • Bayesian logistic regression - allows identification of renalexin response modules from MRSA-252 preteome and transcriptome profiling.
    • Relaxin displayed killing mechanisms & cell wall activity.
      • Gene disruption and osmotic fragility experiments supported cell wall effects.
    • 22 Virulence factors inferred --> VraRS two-component system & PhoU-mediated persister formation --> MRSA tolerance to cationic antimicrobial peptides.
  • Conclusions
    • Integrative approach to study drug resistance and their mode of action. Finds lead to development of trategies against Staphylococcus aureus (MRSA in particular)

Background

  • MRSA - major cause of mortality and mobility. Resistant strains to treatments continue to emerge. Global problem --> community-associated MRSA.
    • Prevention and treatment is needed!
  • Antimicrobial peptides (AMPs) - novel antibiotic --> could be developed to combat bacteria that is resistant (such as MRSA).
    • Produces by all living creatures for defenses -- 880 have been described.
  • Renalexin
    • 20 a.a. peptide (cationic)
    • Possesses single intramolecular dispulphide bond --> forming heptapeptide ring at carboxyl terminus.
    • Displays strong activity against Staphylococcus aureus (Gram-positive bacteria).
    • Offers potential against staphylococcal infections (including MRSA).
  • Need to understand antimicrobial action mechanisms to develop strategies.
  • Antimicrobial inhibitory action can by studied by transcriptome and proteome profiling.
  • Generation of protein and mRNA in response to antimicrobial stress are shown in certain cell functions and provide stress type imposed.
  • Modeled pathway relationships for 95% of S. aureus MRSA-252 genes by integrating proteome and transcriptome profiling of bacteria that was drug-exposed w/ high-confidence functional association network.
    • Approach showed 22 virulence factors and killing mechs. for renalexin along with cell wall effects.
    • Evidence of VraRS two-component system in cationic peptide resistance.
  • Drug target candidate - FtsH. Role of PhoU-mediated persister formation in S. aureus drug tolerance.

Results and Discussion

Renalexin elicits significant changes in transcript and protein levels

  • Sublethal ranalexin impaired but didn't abolish growth of MRSA-252 at concentration of 20μg/ml.
  • Proteome and transcriptome profiling applied between control and renalexin exposed MRSA-252 cultures. Microarrays showed:
    • 93 upregulated genes.
    • 105 downregulated genes.
      • No inconsistencies shown
  • Gene Ontology (GO) --> only few cases of overlap and not uncommon. Identified 290 enriched terms --> highlighting effects of renalexin on MRSA.

Global gene functional association network

  • Developed to give probabilistic model of global gene fn. and lay framework for renalexin response profiles.
  • MRSA-252 genes were network nodes and cell signalling and metabolism were the connections (edges) between genes (nodes).
  • 2494 nodes (genes) and 19076 edges (connections) were contained in final network. Network edges rate was 94.5% of MRSA-252 genes.
  • Hierarchical structure w/ embedded modularity are denoted from node pair degree connectivity along with network degree clustering coefficient distributions.
  • When compared to protein interaction networks, gene functional association is closer to metabolic networks.
    • Seems reasonable because gene interactions are shared amongst all members of a functional group.
  • Network was clustered into 597 putative functional modules --> transcriptome and proteome were mapped into these --> 11 modules had rich genes that showed altered expression in MRSA-252 cultures that were exposed to renalexin.
    • Of theses 11 --> 5 upregulated and 6 downregulated.
    • 58 nodes classified as intermodular hubs that are important regulators of system behavior.

Impact on virulence and inference of novel determinants

  • Upon renalexin exposure(RanaDown), genes significantly downregulated that included all 6 MRSA-353 ESAT-6 secretion system components --> central to Staphylococcus aureus pathogenesis.
  • Significant module included five ESAT-6 components; sixth gene (esaA, SAR0280) not assigned to module. 2 RanaDown genes (SAR0287, SAR0288) - uncharacterized hypothetical proteins.
  • Six transmembrane regions predicted from SAR0280 gene --> 'membrane ABC permease' match found.
  • Predicted that SAR0287 was cell wall anchored or secreted --> also matched conserved domains of protein families and virulence-associated families.
  • Other five genes on module matched conserved domains of unknown fn.
  • TMHMM2 showed one transmembrane protein and two secreted/cell wall.
  • Module showed good correspondence w/ operon structure --> 7 hypothetical genes may be co-regulated with the ESAT-6 system.
  • Two RanaDown modules (4/5 RanaDown; 4/9 RanaDown) had high-affinity metal ion transport --> crucial for establishment of infection.
    • 4/5 RanaDown genes included SAR0787-SAR0790 --> displaying the sst iron-uptake. 5 gene was binding protein for iron complex transport.
  • 12 genes associated with virulence function found in another module (4/16 nodes RanaDown).
    • 12 implicated Colonization and immuno-modulation.
    • Remaining 4 genes: SAR1489, SAR2421, SAR1223, and SAR1802.
    • All 16 genes encode transmembrane/secreted proteins that are anchored on the cell wall.
  • 'Pathogenesis' was significant for this module. Virulence-coupled autolysis for SAR2421, SAR1223, and SAR1802.


10 Biological Terms

  1. Virulence - the degree or ability of a pathogenic organism to cause disease. [Biology Online] 09 November 2011
  2. Putative Substrate - Commonly thought or deemed; supposed; reputed. [Biology Online] 09 November 2011
  3. Cationic - referring to positively charged ions and their properties. [Biology Online] 09 November 2011
  4. Gene Ontology - That department of the science of metaphysics which investigates and explains the nature and essential properties and relations of all beings, as such, or the principles and causes of being. [Biology Online] 09 November 2011
  5. Autolysis - breakdown of whole cell or tissue by self produced enzymes. [Biology Online] 09 November 2011
  6. Staphylococcus aureus - genus of nonmotile gram-positive bacteria that are found in clusters and that produce important exotoxins. Staphylococcus aureus (Staphylococcus pyogenes) is pyogenic, an opportunistic pathogen and responsible for a range of infections including severe sepsis, pneumonia, endocarditis and soft tissue infections. It has protein A on the surface of the cell wall. Coagulase production correlates with virulence: hyaluronidase, lipase and staphylokinase are released in addition to the toxins. [Biology Online] 09 November 2011
  7. Antimicrobia - a drug for killing microorganisms or suppressing their multiplication or growth. An agent (as heat or radiation or a chemical) that destroys microorganisms that might carry disease.An agent (as heat or radiation or a chemical) that destroys microorganisms that might carry disease.[Biology Online] 09 November 2011
  8. Chaperones - cytoplasmic proteins of both prokaryotes and eukaryotes that bind to nascent or unfolded polypeptides and ensure correct folding or transport. Chaperone proteins do not covalently bind to their targets and do not form part of the finished product. Heat-shock proteins are an important sub set of chaperones. [Biology Online] 09 November 2011
  9. Ranalexin
  10. Vancomycin

Links

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Alex_A._Cardenas_Week_11&oldid=565659"