THE PUZZLING PROPERTIES OF THE PERMEASE (PPP)
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THE PUZZLING PROPERTIES OF THE PERMEASE (PPP) Kim Finer, Jennifer Galovich, Ruth Gyure, Dave Westenberg March 4, 2006. IS THERE AN E.COLI -TYPE IRON PERMEASE GENE (FepD) IN CHROMOHALOBACTER SP . AND IF SO, IS THE PERIPLASMIC-FACING RESIDUE SEQUENCE SIGNIFICANTLY DIFFERENT?.

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THE PUZZLING PROPERTIES OF THE PERMEASE (PPP)Kim Finer, Jennifer Galovich, Ruth Gyure, Dave WestenbergMarch 4, 2006


IS THERE AN E.COLI-TYPE IRON PERMEASE GENE (FepD) IN CHROMOHALOBACTER SP. AND IF SO, IS THE PERIPLASMIC-FACING RESIDUE SEQUENCE SIGNIFICANTLY DIFFERENT?


BACKGROUND:Escherichia coli is known to have a ferric citrate transport system involving outer membrane permease, periplasmic transporters and an inner transmembrane protein encoded by the gene fepD. The fepD gene can also be found in other gram negative bacteria such as Pseudomonas aeruginosa PAO1.

Chromohalobacter salexigens is a newly described species of bacterium able to survive in moderately saline environments. The species includes the previously described species, Halomonas elongata. One of its survival adaptations is the use of higher percentages of acidic amino acid residues in proteins that come into contact with the high salt environment. This modification protects the proteins from ‘salting out.’

HYPOTHESIS: We predict that transmembrane proteins such as FepD would also demonstrate this characteristic enrichment with acidic residues, but only in the hydrophilic regions facing the salty periplasm. Regions of protein hydrophilic regions facing the cytoplasm would be similar in chargemakeup to the corresponding regions of FepD in E. coli, P. aeruginosa, etc.


http://hugroup.cems.umn.edu/Research/Images_research/Ecoli.jpghttp://hugroup.cems.umn.edu/Research/Images_research/Ecoli.jpg


SALTY ENVIRONMENT, http://hugroup.cems.umn.edu/Research/Images_research/Ecoli.jpg

For Chromobacter

These segments would be the same in the three species

SALTY ENVIRONMENT,

For Chromohalobacter

These segments in Chromohalobacter would be more acidic than in the other two species


Methods
METHODShttp://hugroup.cems.umn.edu/Research/Images_research/Ecoli.jpg

We began by accessing an Excel spreadsheet of annotated C. salexigens sequences available at JGI. The spreadsheet was searched for ferric citrate transporter. The sequence reference was found (NP-415122) and the homologous sequences from E. coli and P. aeruginosa were identified.

The protein sequence for this accession was obtained from the JGI website.

Protein sequences for FepD from E. coli K12 and P. aeruginosa (PAO1) were obtained from the NCBI website.


  • Using Biology Workbench, we uploaded these three aa sequences and used GREASE to reveal the hydrophobicity profile (graph) for each protein chain.

  • Using PI, we obtained the overall isoelectric point at each pH, with our interest being pH7 to compare the three proteins overall. Our hypothesis predicts that Chromohalobacter would have the lowest isoelectric point (more acidic residues).


However, stronger evidence would be obtained by comparing each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.

A third approach was to analyze the sequences using the Excel based analysis program, Protein Analysis. Protein analysis was used to plot the location of acidic amino acid residues along the entire peptide sequence.


E coli data
E. coli each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species. Data


Sequence: each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.

MSGSVAVTRA IAVPGLLLLL IIATALSLLI GAKSLPASVV LEAFSGTCQS ADCTIVLDAR LPRTLAGLLA GGALGLAGAL MQTLTRNPLA DPGLLGVNAG ASFAIVLGAA LFGYSSAQEQ LAMAFAGALV ASLIVAFTGS QGGGQLSPVR LTLAGVALAA VLEGLTSGIA LLNPDVYDQL RFWQAGSLDI RNLHTLKVVL IPVLIAGATA LLLSRALNSL SLGSDTATAL GSRVARTQLI GLLAITVLCG SATAIVGPIA FIGLMMPHMA RWLVGADHRW SLPVTLLATP ALLLFADIIG RVIVPGELRV SVVSAFIGAP VLIFLVRRKT RGGA

Isoelectric Point:

10.476999


Kyte doolittle hydropathy profile
Kyte-Doolittle Hydropathy Profile each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.


Predicted transmembrane segments for e coli
Predicted Transmembrane Segments for each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.E. coli:

  • TM 1: 11 - 39 (29)

  • TM 2: 66 - 86 (21)

  • TM 3: 94 - 114 (21)

  • TM 4: 121 - 143 (23)

  • TM 5: 152 - 173 (22)

  • TM 6: 193 - 221 (29)

  • TM 7: 243 - 271 (29)

  • TM 8: 283 - 303 (21)

  • TM 9: 310 - 330 (21)


Pi of non transmembrane segments
pI of Non-Transmembrane Segments each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.


P aeruginosa data
P. aeruginosa each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species. Data


Sequence: each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.

MQASPMRRRR LRAWGLLAGA LLLALAALAS LALGSRPVPL AVTLDALQAV DPHDDRHLVV RELRLPRTLV ALLAGAALG VAGALMQALT RNPLAEPGLL GINAGAALAV IVGVALFDLA SMGQYLGCAF LGAGLAGIAV FLLGQARETG TNPVRLVLAG AGLSVMLASL TGIIVLNAPP EVFDRFRHWA AGSLSGSGFA

LLGWPGLAIG AGLAAAFALAA RLNALALGQE I GQALGVDLRL

TWLLACLAVM LLAGAATALAG PIAFVGLVAP HLARLLAGPD

QRWILPFSAL IAAGLLLGAD ILGRLLAAPT EIAAGIVALL LGGPAFIVLV RRFRLSRL

Isoelectric Point:

11.822999


Predicted transmembrane segments for p aeruginosa
Predicted Transmembrane Segments for each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.P. aeruginosa:

  • TM 1: 11 - 39 (29)

  • TM 2: 66 - 94 (29)

  • TM 3: 100 - 120 (21)

  • TM 4: 126 - 146 (21)

  • TM 5: 156 - 184 (29)

  • TM 6: 202 - 226 (25)

  • TM 7: 246 - 274 (29)

  • TM 8: 289 - 309 (21)

  • TM 9: 316 - 336 (21)


Kyte doolittle hydropathy profile1
Kyte-Doolittle Hydropathy Profile each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.


Pi of non transmembrane segments1
pI of Non-Transmembrane Segments each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.


C salexigens data
C. salexigens each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species. Data


Sequence: each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.

MLTRRTTRLA GLLAGLVLMA TTFAASVMLG TTELPPSTFI ATLLHYDPSR VAHIIIVKER LPRAVIAVLV GASLAIAGTL MQTLTRNPLA SPGILGINAG AMCFVVIAVA LLPLHAPADY

VWAALLGALV AACLVLMLSR GGGRAGPSSL RVVLAGVAVT AMFVSFSQGL LIIDHQSFES VLYWLAGSVS GRELSLVVPL LPLFGIALLL CMLLVRHANA LMLGDDMVTS LGMHAGTIKL LLGLVVILLA GSSVALTGMI GFVGLIVPHM ARGLFGFDHR WLLPACALLG ACLLLLADVA SRFLMPPQDV PVGVMTALIG TPFFIYLARR QQARP

Isoelectric Point:

9.970999


Predicted transmembrane segments for c salexigens
Predicted Transmembrane Segments for each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.C. salexigens:

  • TM 1: 5 - 33 (29)

  • TM 2: 62 - 90 (29)

  • TM 3: 96 - 116 (21)

  • TM 4: 122 - 142 (21)

  • TM 5: 150 - 177 (28)

  • TM 6: 194 - 222 (29)

  • TM 7: 242 - 270 (29)

  • TM 8: 281 - 308 (28)


Kyte doolittle hydropathy profile2
Kyte-Doolittle Hydropathy Profile each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.


Pi of non transmembrane segments2
pI of Non-Transmembrane Segments each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.


Comparison of pi data
Comparison of pI Data each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.


Protein analysis program plot of acidic amino acids e coli
Protein Analysis Program plot of acidic amino acids - each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species. E. coli


Protein analysis program plot of acidic amino acids p aeruginosa
Protein Analysis Program plot of acidic amino acids each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species. - P. aeruginosa


Protein analysis program plot of acidic amino acids c salexigens
Protein Analysis Program plot of acidic amino acids each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species. - C. salexigens


Conclusions
CONCLUSIONS each hydrophilic region in a pairwise fashion. TMAP allowed us to obtain a more precise prediction of which segments were hydrophobic vs. hydrophilic. There were 9 predicted transmembrane regions. Finally, each hydrophilic segment was submitted for PI analysis and the isoelectric point for each segment was compared among the three species.

Hydropathy plots illustrate a similar topology for the FepD proteins of C. salexigens, E.coli and P. aeruginosa. We predicted that the loop domains or the C. salexigens FepD protein, exposed to the exterior of the cell would have a lower pI than the exterior domains of E. coli and P. aeruginosa. The calculated pI of the entire C. salexigens FepD protein is lower than the pI of the other two organisms. However, the calculated pI of individual loop domains and a plot of acidic residues show that the overall hypothesis is not supported. Several loop domains of the C. salexigens FepD protein have a lower calculated pI than the corresponding segments of E. coli, However, comparison to the corresponding domains of the P. aeruginosa FepP protein do not show the same trend. In fact, P. aeruginosa seems to have more acidic loop domains than C. salexigens.


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