Difference between revisions of "Kevinmcgee Week 11"

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glycoinositol-phospholipids
 
glycoinositol-phospholipids
 
prenylation
 
prenylation
 +
 +
 +
=Leishmania Background=
 +
#Leishmania Major is a tropical parasite
 +
#Sepctrum of disease, “Leishmaniases”
 +
#*broad term describing a flesh eating virus specific to Leishmania
 +
#*2 million infections in 88 countries annually
 +
#Have adapted to avoid host destruction
 +
#*curing is very hard and doesn’t always work
 +
=Genome Structure and Content=
 +
#32,816,678 base pairs obtained
 +
#36 chromosomes
 +
#*single continuous sequence generated for each chromosome
 +
#911 RNA genes
 +
#*Organized differently in Tritryp genomes from L. Major
 +
#8272 protein coding genes
 +
#663 related families
 +
#*Smaller gene families arose from gene duplication
 +
#*Larger families have single genes at multiple locations on the gene
 +
=Genome Comparison=
 +
#Leishmania is compared with other organisms
 +
#*Trypanosoma Brucei
 +
#*Trypanosoma Cruzi
 +
#*Leishmania has many orthologs under in these genomes
 +
#910 genes not orthologs
 +
#*“Leishmania Restricted genes”
 +
#**responsible for key metabolic differences
 +
#LmjF33.1740 and LmjF33.1750
 +
#*Macrophage migration inhibition factor
 +
#**Similar to that in humans that deals with immunity from macrophage
 +
=Significant Genetic Findings=
 +
==Transcription==
 +
#L. major genome is organized into 133 clusters of tens to hundreds of protein-coding genes on same DNA strand
 +
#Pollycistronic transcription initiates in both directions:
 +
#*In divergent strand-switch regions
 +
#*terminates within the convergent strand-switch regions
 +
#RNAP I, II and III were found in Trytrip
 +
#*Very different from other eukaryotes
 +
#Not many other homologs of RNAP were found
 +
#These findings, along with the polycistronic gene organization, are consistent with posttranscriptional control mechanisms being the primary determinants of Tritryp gene expression
 +
==RNA Processing==
 +
#Polyadenylation is determined by trans-splicing of downstream mRNA
 +
#Tritryp Poly (A) polymerases
 +
#*two distinct ones with different functional roles
 +
#**Homologs of CPF are present
 +
#**No homologs of CstF are present except for CstF50
 +
#***CstF50 deals with poyadenylation and transcription initiation/termination
 +
#***reflects polycistronic transcription
 +
#Degredation of mRNA is important in gene expression
 +
#*Exonucleases involved in decapping of mRNA were found.
 +
# All of these imply reliance on posttranscriptional control of gene expression
 +
==Translation and co-/postranslational modification==
 +
#Translation machinery are found withing the tritryps
 +
#*large amount of elF-4A gene
 +
#**Implies nucleic acid binding
 +
#Protein Modification steps
 +
#*phosphorylation
 +
#*glycosylation
 +
#*lipidation
 +
#Essential modifications
 +
#*glycosylphosphatidylinositol anchor addition
 +
#*acytlation
 +
#*protein-protein interaction
 +
#*Enzymes that catalyze these modifications are potential drug targets
 +
==Surface molecules==
 +
#Surface molecules are very important in the infection process
 +
#*lipophosphoglycan (LPG)
 +
#**assembled in the lumen of the golgi apparatus
 +
#**entire synthetic pathway has not been fully mapped
 +
#*glycoinositol-phospholipids (GIPLs)
 +
#*membrane proteophosphoglycan (PPG)
 +
#*glycosylated GPI-anchored proteins
 +
#Sphingolipids are essential membrane componenets of eukaryotes
 +
#*good drug targets
 +
==Proteolysis==
 +
#Peptidases have already been identified as virulence factors and vaccine candidates
 +
=Implications=
 +
#Tritryp genomes help show unique biology of Leishmania and give insight to Eukaryote evolution
 +
#*Leishmania branched off from other eukaryotes very early on
 +
#*Differences arose after branching off of Leishmania
 +
#Differences from other eukaryotes: posttranslational modification
 +
#*polycistronic gene clusters
 +
#*mRNA trans-splicing coupled with polyadenylation
 +
#Full genome provides crucial information for new therapies of Leishmaniasis
 +
#*analysis of virulence factors
 +
#*enzymes in metabolic pathways
 +
#*potential vaccine candidates
 +
 +
=TritrypDB=
 +
#Contains mostly sequences that are manually added by the community. It is a meta database.
 +
#It is held under the EuPathDB Bioinformatics Resource Center
 +
#Funded by the Bill and Melinda Gates Foundation and the Welcome Trust
 +
#Database is free and open to the public as long as proper citation is included
 +
#Updated as new information comes in. Last update was in September of this year
 +
#Yes. There are links to other databases on every organism that is on the site.
 +
#Files can be downloaded in FAFSTA and gff.
 +
#The database was somewhat friendly. It is organized well enough and there is a help section, but things are very clearly defined to me and I got lost easily. The eample querry gave me what I was looking for, but when I typed into Leishmania Major the actual data for L. Major was far down the page.
 +
#LmjF.##.###
 +
 +
[[Leishmania major]]
 +
 +
[[User:Kevinmcgee|Kevinmcgee]] ([[User talk:Kevinmcgee|talk]]) 22:07, 11 November 2013 (PST)

Latest revision as of 06:07, 12 November 2013

trypanosomatid Ecotins chymotrypsin amastins Sphingolipids PG-galactosyltransferases pseudogenes ribonuclease glycoinositol-phospholipids prenylation


Contents

[edit] Leishmania Background

  1. Leishmania Major is a tropical parasite
  2. Sepctrum of disease, “Leishmaniases”
    • broad term describing a flesh eating virus specific to Leishmania
    • 2 million infections in 88 countries annually
  3. Have adapted to avoid host destruction
    • curing is very hard and doesn’t always work

[edit] Genome Structure and Content

  1. 32,816,678 base pairs obtained
  2. 36 chromosomes
    • single continuous sequence generated for each chromosome
  3. 911 RNA genes
    • Organized differently in Tritryp genomes from L. Major
  4. 8272 protein coding genes
  5. 663 related families
    • Smaller gene families arose from gene duplication
    • Larger families have single genes at multiple locations on the gene

[edit] Genome Comparison

  1. Leishmania is compared with other organisms
    • Trypanosoma Brucei
    • Trypanosoma Cruzi
    • Leishmania has many orthologs under in these genomes
  2. 910 genes not orthologs
    • “Leishmania Restricted genes”
      • responsible for key metabolic differences
  3. LmjF33.1740 and LmjF33.1750
    • Macrophage migration inhibition factor
      • Similar to that in humans that deals with immunity from macrophage

[edit] Significant Genetic Findings

[edit] Transcription

  1. L. major genome is organized into 133 clusters of tens to hundreds of protein-coding genes on same DNA strand
  2. Pollycistronic transcription initiates in both directions:
    • In divergent strand-switch regions
    • terminates within the convergent strand-switch regions
  3. RNAP I, II and III were found in Trytrip
    • Very different from other eukaryotes
  4. Not many other homologs of RNAP were found
  5. These findings, along with the polycistronic gene organization, are consistent with posttranscriptional control mechanisms being the primary determinants of Tritryp gene expression

[edit] RNA Processing

  1. Polyadenylation is determined by trans-splicing of downstream mRNA
  2. Tritryp Poly (A) polymerases
    • two distinct ones with different functional roles
      • Homologs of CPF are present
      • No homologs of CstF are present except for CstF50
        • CstF50 deals with poyadenylation and transcription initiation/termination
        • reflects polycistronic transcription
  3. Degredation of mRNA is important in gene expression
    • Exonucleases involved in decapping of mRNA were found.
  4. All of these imply reliance on posttranscriptional control of gene expression

[edit] Translation and co-/postranslational modification

  1. Translation machinery are found withing the tritryps
    • large amount of elF-4A gene
      • Implies nucleic acid binding
  2. Protein Modification steps
    • phosphorylation
    • glycosylation
    • lipidation
  3. Essential modifications
    • glycosylphosphatidylinositol anchor addition
    • acytlation
    • protein-protein interaction
    • Enzymes that catalyze these modifications are potential drug targets

[edit] Surface molecules

  1. Surface molecules are very important in the infection process
    • lipophosphoglycan (LPG)
      • assembled in the lumen of the golgi apparatus
      • entire synthetic pathway has not been fully mapped
    • glycoinositol-phospholipids (GIPLs)
    • membrane proteophosphoglycan (PPG)
    • glycosylated GPI-anchored proteins
  2. Sphingolipids are essential membrane componenets of eukaryotes
    • good drug targets

[edit] Proteolysis

  1. Peptidases have already been identified as virulence factors and vaccine candidates

[edit] Implications

  1. Tritryp genomes help show unique biology of Leishmania and give insight to Eukaryote evolution
    • Leishmania branched off from other eukaryotes very early on
    • Differences arose after branching off of Leishmania
  2. Differences from other eukaryotes: posttranslational modification
    • polycistronic gene clusters
    • mRNA trans-splicing coupled with polyadenylation
  3. Full genome provides crucial information for new therapies of Leishmaniasis
    • analysis of virulence factors
    • enzymes in metabolic pathways
    • potential vaccine candidates

[edit] TritrypDB

  1. Contains mostly sequences that are manually added by the community. It is a meta database.
  2. It is held under the EuPathDB Bioinformatics Resource Center
  3. Funded by the Bill and Melinda Gates Foundation and the Welcome Trust
  4. Database is free and open to the public as long as proper citation is included
  5. Updated as new information comes in. Last update was in September of this year
  6. Yes. There are links to other databases on every organism that is on the site.
  7. Files can be downloaded in FAFSTA and gff.
  8. The database was somewhat friendly. It is organized well enough and there is a help section, but things are very clearly defined to me and I got lost easily. The eample querry gave me what I was looking for, but when I typed into Leishmania Major the actual data for L. Major was far down the page.
  9. LmjF.##.###

Leishmania major

Kevinmcgee (talk) 22:07, 11 November 2013 (PST)

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