Difference between revisions of "Karen's Assignment"

From GcatWiki
Jump to: navigation, search
 
(39 intermediate revisions by 2 users not shown)
Line 1: Line 1:
'''Potassium homeostasis'''
+
'''Potassium homeostasis''' ([http://gcat.davidson.edu/GcatWiki/images/c/c6/Potassium_homeostasis_presentation.ppt Download PPT Presentation])
  
 
'''How does our species maintain potassium homeostasis?'''
 
'''How does our species maintain potassium homeostasis?'''
  
In JGI's list of genes with predicted functions, I found the following 10 genes related to K+:<br>
+
In JGI's list of genes with predicted functions, I found the following 10 genes related to K+ (6 of which were called in RAST):<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032472 K+ transport system, NAD-binding component]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032472 K+ transport system, NAD-binding component]<br>
 +
 +
2603205..2603861(+)
 +
 +
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.2683 Trk system potassium uptake protein trkA-1]<br>
 +
 +
Start 2603205 <br>
 +
Stop 2603861 <br>
 +
[[Image:Trk system potassium uptake protein.png]] <br>
 +
This is the same as a JGI called gene.
 +
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032048 K+ transport system, NAD-binding component]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032048 K+ transport system, NAD-binding component]<br>
 +
 +
2199065..2199751(+)
 +
 +
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.2260 Trk system potassium uptake protein trkA-3]<br>
 +
 +
Start 2199116 <br>
 +
Stop 2199751 <br>
 +
[[Image:Trk system potassium uptake protein-3.png]] <br>
 +
Similar to a JGI called gene, but the start position is later in RAST than JGI.
 +
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032061 K+ transport system, NAD-binding component]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032061 K+ transport system, NAD-binding component]<br>
 +
 +
2210390..2211088(-)
 +
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032129 Kef-type K+ ransport system, predicted NAD-binding component]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032129 Kef-type K+ ransport system, predicted NAD-binding component]<br>
 +
 +
2271340..2272527(+)
 +
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032854 Kef-type K+ transport system, membrane component]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032854 Kef-type K+ transport system, membrane component]<br>
 +
 +
2954301..2955512(+)
 +
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644031768 K+ transport system, NAD-binding component]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644031768 K+ transport system, NAD-binding component]<br>
 +
 +
1938027..1939364(-)
 +
 +
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.1990 Trk system potassium uptake protein trkA-4]<br>
 +
 +
Start 1939364 <br>
 +
Stop 1938027 <br>
 +
[[Image:Trk system potassium uptake protein-4.png]] <br>
 +
This is the same as a JGI called gene.
 +
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644031769 Trk-type K+ transport system, membrane component]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644031769 Trk-type K+ transport system, membrane component]<br>
 +
 +
1939429..1940991(-)
 +
 +
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.1991 Potassium uptake protein TrkH]<br>
 +
 +
Start 1940991 <br>
 +
Stop 1939429 <br>
 +
[[Image:Potassium uptake protein TrkH.png]] <br>
 +
This is the same as a JGI called gene.
 +
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032689 K+ transport system, NAD-binding component]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032689 K+ transport system, NAD-binding component]<br>
 +
 +
2797145..2798779(-)
 +
 +
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.2901 Potassium channel protein-1]<br>
 +
 +
Start 2798779 <br>
 +
Stop 2797145 <br>
 +
[[Image:Potassium channel protein-1.png]] <br>
 +
This is the same as a JGI called gene.
 +
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644030929 K+ transport system, NAD-binding component]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644030929 K+ transport system, NAD-binding component]<br>
 +
 +
1146592..1148280(-)
 +
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032916 NhaP-type Na+(K+)/H+ antiporter]<br>
 
[http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032916 NhaP-type Na+(K+)/H+ antiporter]<br>
 +
 +
3021102..3022994(+)
 +
 +
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.3126 Trk system potassium uptake protein trkA-2]<br>
 +
 +
Start 3021102 <br>
 +
Stop 3022994 <br>
 +
[[Image:Trk system potassium uptake protein-2.png]] <br>
 +
This is the same as a JGI called gene.
  
 
I found no genes with predicted functions that are associated with Cl- from JGI<br>
 
I found no genes with predicted functions that are associated with Cl- from JGI<br>
  
In RAST, I found seven distinct genes (some of which were called multiple times) related to potassium homeostasis:<br>
+
In RAST, I found seven genes related to potassium homeostasis that were not called in JGI:<br>
 +
 
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.2354 Cobalt-zinc-cadmium resistance protein]<br>
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.2354 Cobalt-zinc-cadmium resistance protein]<br>
 +
 +
Start: 2285691 <br>
 +
Stop: 2284783 <br>
 +
[[Image:Cobalt-zinc-cadmium resistance protein.png]]
 +
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.700 Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) / Phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3)]<br>
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.700 Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) / Phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3)]<br>
 +
 +
Start 678963 <br>
 +
Stop 680573 <br>
 +
[[Image:Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2).png]]
 +
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.2686 Hydroxyacylglutathione hydrolase (EC 3.1.2.6)-1]<br>
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.2686 Hydroxyacylglutathione hydrolase (EC 3.1.2.6)-1]<br>
 +
 +
Start 2604831 <br>
 +
Stop 2605442 <br>
 +
[[Image:Hydroxyacylglutathione hydrolase (EC 3.1.2.6).png]]
 +
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.1319 Hydroxyacylglutathione hydrolase (EC 3.1.2.6)-2]<br>
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.1319 Hydroxyacylglutathione hydrolase (EC 3.1.2.6)-2]<br>
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.2683 Trk system potassium uptake protein trkA-1]<br>
+
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.3126 Trk system potassium uptake protein trkA-2]<br>
+
Start 1276452 <br>
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.2260 Trk system potassium uptake protein trkA-3]<br>
+
Stop 1277027 <br>
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.1990 Trk system potassium uptake protein trkA-4]<br>
+
[[Image:Hydroxyacylglutathione hydrolase (EC 3.1.2.6)-2.png]]
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.1991 Potassium uptake protein TrkH]<br>
+
 
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.1476 Kef-type K+ transport systems (NAD-binding component fused to domain related to exopolyphosphatase)-1]<br>
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.1476 Kef-type K+ transport systems (NAD-binding component fused to domain related to exopolyphosphatase)-1]<br>
 +
 +
Start 1431353 <br>
 +
Stop 1429968 <br>
 +
[[Image:potassium_transport_systems-1.png]] <br>
 +
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.1703 Kef-type K+ transport systems (NAD-binding component fused to domain related to exopolyphosphatase)-2]<br>
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.1703 Kef-type K+ transport systems (NAD-binding component fused to domain related to exopolyphosphatase)-2]<br>
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.2901 Potassium channel protein-1]<br>
+
 
 +
Start 1650228 <br>
 +
Stop 1648756 <br>
 +
[[Image:potassium_transport_systems-2.png]] <br>
 +
 
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.3028 Potassium channel protein-2]<br>
 
[http://rast.nmpdr.org/seedviewer.cgi?page=Annotation&feature=fig|485914.5.peg.3028 Potassium channel protein-2]<br>
 +
 +
Start 2916660 <br>
 +
Stop 2915455 <br>
 +
[[Image:Potassium channel protein-2.png]] <br>
  
 
I found no genes with predicted functions that are associated with Cl- function on RAST.
 
I found no genes with predicted functions that are associated with Cl- function on RAST.
Line 99: Line 199:
 
  [[Image:Pharaonis_3.png]]
 
  [[Image:Pharaonis_3.png]]
 
  [[Image:Pharaonis_4.png]]
 
  [[Image:Pharaonis_4.png]]
 +
 +
Blastn results for [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644031769 Trk-type K+ transport system, membrane component]<br>
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=BJ9VZPHM01N&log%24=nuclalign&blast_rank=2&list_uids=76556520 Natronomonas pharaonis DSM 2160 complete genome]
 +
[[Image:pharaonis_5.png]]
 +
[[Image:pharaonis_6.png]]
 +
[Halorubrum lacusprofundi ATCC 49239 chromosome 1, complete sequence http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=BJ9VZPHM01N&log%24=nuclalign&blast_rank=3&list_uids=222451341]
 +
[[Image:lacusprofundi_7.png]]
 +
[[Image:lacusprofundi_8.png]]
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=BJ9VZPHM01N&log%24=nuclalign&blast_rank=4&list_uids=55229667 Haloarcula marismortui ATCC 43049 chromosome I, complete sequence]
 +
[[Image:Marismortui_10.png]]
 +
[[Image:Marismortui_11.png]]
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=BJ9VZPHM01N&log%24=nuclalign&blast_rank=5&list_uids=167728580 Halobacterium salinarum PHS3 plasmid complete genome, strain]
 +
[[Image:Salinarum_5.png]]
 +
[[Image:Salinarum_6.png]]
 +
 +
Blastn results for [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032689 K+ transport system, NAD-binding component]<br>
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=BJAPEN4S01N&log%24=nuclalign&blast_rank=2&list_uids=55229667 Haloarcula marismortui ATCC 43049 chromosome I, complete sequence]
 +
[[Image:Marismortui_12.png]]
 +
[[Image:Marismortui_13.png]]
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=BJAPEN4S01N&log%24=nuclalign&blast_rank=3&list_uids=167726115 Halobacterium salinarum complete genome, strain R1]
 +
[[Image:Salinarum_7.png]]
 +
[[Image:Salinarum_8.png]]
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=BJAPEN4S01N&log%24=nuclalign&blast_rank=4&list_uids=12057215 Halobacterium sp. NRC-1, complete genome]
 +
[[Image:NRC-1_5.png]]
 +
[[Image:NRC-1_6.png]]
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=BJAPEN4S01N&log%24=nuclalign&blast_rank=6&list_uids=222451341 Halorubrum lacusprofundi ATCC 49239 chromosome 1, complete sequence]
 +
[[Image:lacusprofundi_9.png]]
 +
[[Image:lacusprofundi_10.png]]
 +
 +
The blastn results are becoming very repetitive. I think at this point, the way to attack this problem may be to look into this list of 5-6 species that seem to share the potassium proteins seen in our species. If I can find a common thread in how other species are utilizing the same potassium homeostasis machinery, it will tell me a great deal about how our own species is using all these potassium related genes.
  
 
It is important to note that many of these genes were also related to the species Halorhabdus utahensis. I did not include the blastn results for this species because Blast could not specify which gene segment these matches were a part of. I believe this was not included simply because this species has not been annotated (or the annotation has not been entered into blast). In any comparison of species that takes place after this, I will need to include this species as well.
 
It is important to note that many of these genes were also related to the species Halorhabdus utahensis. I did not include the blastn results for this species because Blast could not specify which gene segment these matches were a part of. I believe this was not included simply because this species has not been annotated (or the annotation has not been entered into blast). In any comparison of species that takes place after this, I will need to include this species as well.
Line 106: Line 236:
 
"Cell membranes are freely permeable to water, so the only way to prevent the loss of cellular water under high salt conditions is to increase the internal solute concentration. Halotolerantand halophilic microorganisms therefore accumulate high solute concentrations within the cytoplasm." [http://brent.xner.net/BIOL4125/Lectures/BIOL4125_S09_L24-HaloArch.pdf]
 
"Cell membranes are freely permeable to water, so the only way to prevent the loss of cellular water under high salt conditions is to increase the internal solute concentration. Halotolerantand halophilic microorganisms therefore accumulate high solute concentrations within the cytoplasm." [http://brent.xner.net/BIOL4125/Lectures/BIOL4125_S09_L24-HaloArch.pdf]
  
I am beginning to understand potassium homeostasis and how it may be useful to our organism to survive in high salt concentrations by first researching how other known species utilize this mechanism. In a paper by [http://illiad.davidson.edu/pdf/40335.pdf Strahl and Greie], the Halobacterium salinarum species use of potassium homeostasis to maintain life in a high salinity environment is described. Apparently these organisms maintain life in such conditions by creating an equimolar condition within their cytoplasm. KCl is the preferred ion to create this equal osmolality for this halobacterium resulting in osmotic equilibrium with the surrounding environment. The K+ ion enters the cell by both passive transport mechanisms as well as active transport mechanisms. A gene, kdpFABC, has been discovered in this organism that codes for homologs of a bacterial APT-driven K+ uptake system. Deletion of this gene is detrimental to organism survival in limiting K+ conditions. This paper also mentions that this mechanism is unique to this and another species of halobacterium because other halophiles utilize organic solutes to equalize osmotic pressures in high salinity environments. I must determine whether or not potassium homeostasis could be a mechanism of maintaining osmotic equilibrium in our species.
+
I am beginning to understand potassium homeostasis and how it may be useful to our organism to survive in high salt concentrations by first researching how other known species utilize this mechanism. In a paper by [http://illiad.davidson.edu/pdf/40335.pdf Strahl and Greie], the Halobacterium salinarum species use of potassium homeostasis to maintain life in a high salinity environment is described. Apparently these organisms maintain life in such conditions by creating an equimolar condition within their cytoplasm. KCl is the preferred ion to create this equal osmolality for this halobacterium resulting in osmotic equilibrium with the surrounding environment. The K+ ion enters the cell by both passive transport mechanisms as well as active transport mechanisms. A gene, kdpFABC, has been discovered in this organism that codes for homologs of a bacterial ATP-driven K+ uptake system. Deletion of this gene is detrimental to organism survival in limiting K+ conditions. This paper also mentions that this mechanism is unique to this and another species of halobacterium because other halophiles utilize organic solutes to equalize osmotic pressures in high salinity environments. I must determine whether or not potassium homeostasis could be a mechanism of maintaining osmotic equilibrium in our species.
  
 
A paper by [http://illiad.davidson.edu/pdf/40339.pdf Oren et al.] describes another species, Salinibacter ruber, that appears to be capable of surviving in high salinity environments due to the uptake of high concentrations of potassium. The finding that potassium homeostasis seems to be the mechanism of maintaining life in a high salinity environment was determined by measuring K+, Cl+, glutamate, glycine betaine, and N-alpha-acetyllysine concentrations within the cytoplasm. High amounts of K+ and Cl+ were found within the cytoplasm but low amounts of glutamate, glycine betaine, and N-alpha-acetyllysine were discovered. These three organic solutes are often associated with maintaining osmotic equilibrium in archaic halophiles that exist in high salinity environments. It is unusual that this species does not utilize these organic solutes to maintain homeostasis but instead seems to be utilizing the inorganic molecule KCl. This paper provides another example of potassium concentrations being utilized to maintain life in high salinity environments. I need to determine if our species is using this inorganic molecule or the more common organic molecules to maintain osmotic balance in a high salinity environment.
 
A paper by [http://illiad.davidson.edu/pdf/40339.pdf Oren et al.] describes another species, Salinibacter ruber, that appears to be capable of surviving in high salinity environments due to the uptake of high concentrations of potassium. The finding that potassium homeostasis seems to be the mechanism of maintaining life in a high salinity environment was determined by measuring K+, Cl+, glutamate, glycine betaine, and N-alpha-acetyllysine concentrations within the cytoplasm. High amounts of K+ and Cl+ were found within the cytoplasm but low amounts of glutamate, glycine betaine, and N-alpha-acetyllysine were discovered. These three organic solutes are often associated with maintaining osmotic equilibrium in archaic halophiles that exist in high salinity environments. It is unusual that this species does not utilize these organic solutes to maintain homeostasis but instead seems to be utilizing the inorganic molecule KCl. This paper provides another example of potassium concentrations being utilized to maintain life in high salinity environments. I need to determine if our species is using this inorganic molecule or the more common organic molecules to maintain osmotic balance in a high salinity environment.
 +
 +
'''H. salinarum K+ transport mechanism comparison'''
 +
Found the nucleotide sequence for the KdpFABC operon in the species H. salinarum using NCBI. Compared this sequence to our species genome using Blastx. Found three significant hits:
 +
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=C4DEM387014&log%24=protalign&blast_rank=1&list_uids=257372919 heavy metal translocating P-type ATPase-1] <br>
 +
[[Image:heavy metal translocating P-type ATPase-1.png]]
 +
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=C4DEM387014&log%24=protalign&blast_rank=2&list_uids=257388732 heavy metal translocating P-type ATPase-2] <br>
 +
[[Image:heavy metal translocating P-type ATPase-2.png]]
 +
 +
[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=C4DEM387014&log%24=protalign&blast_rank=3&list_uids=257373045 heavy metal translocating P-type ATPase-3] <br>
 +
[[Image:heavy metal translocating P-type ATPase-3.png]]
 +
 +
These hits could just be related to the ATPase function of the Kdp operon in H. salinarum and have nothing to do with potassium transport. I am going to redo this blastx with individual genes from operon Kdp compared to our species genome separately. When blasted separately, I found that the three hits from above were in the gene KdpB in the operon of H salinarum. No other similarities, however, were discovered.
 +
 +
'''Other species potassium uptake systems'''
 +
For the 6 other species that have similar potassium related genes to our species (Halorhabdus utahensis, Halorubrum lacusprofundi, Halobacterium sp. NRC-1, Haloarcula marismortui, Natronomonas pharaonis, & Halogeometricum borinquense. Excluding Halobacterium salinarum since I already compared the KdpFABC operon), I reviewed literature and did pubmed searches trying to find anything that would relate potassium to these species. The only time I found potassium mentioned in conjunction with one of these species was when one website said that Halobacterium sp. NRC-1 has potassium uptake systems coded for in its genome [http://microbewiki.kenyon.edu/index.php/Halobacterium_sp._NRC-1 Kenyon MicrobeWiki]. Since this was the only time potassium was mentioned in conjunction with any of these species, it is unlikely that potassium is essential for the survival of these species. Because of this fact and the lack of evidence of the KdpFABC operon in our species genome, it seems unlikely that potassium homeostasis is essential for our species survival in high salinity environments.

Latest revision as of 13:21, 1 October 2009

Potassium homeostasis (Download PPT Presentation)

How does our species maintain potassium homeostasis?

In JGI's list of genes with predicted functions, I found the following 10 genes related to K+ (6 of which were called in RAST):
K+ transport system, NAD-binding component

2603205..2603861(+)

Trk system potassium uptake protein trkA-1

Start 2603205
Stop 2603861
Trk system potassium uptake protein.png
This is the same as a JGI called gene.

K+ transport system, NAD-binding component

2199065..2199751(+)

Trk system potassium uptake protein trkA-3

Start 2199116
Stop 2199751
Trk system potassium uptake protein-3.png
Similar to a JGI called gene, but the start position is later in RAST than JGI.

K+ transport system, NAD-binding component

2210390..2211088(-)

Kef-type K+ ransport system, predicted NAD-binding component

2271340..2272527(+)

Kef-type K+ transport system, membrane component

2954301..2955512(+)

K+ transport system, NAD-binding component

1938027..1939364(-)

Trk system potassium uptake protein trkA-4

Start 1939364
Stop 1938027
Trk system potassium uptake protein-4.png
This is the same as a JGI called gene.

Trk-type K+ transport system, membrane component

1939429..1940991(-)

Potassium uptake protein TrkH

Start 1940991
Stop 1939429
Potassium uptake protein TrkH.png
This is the same as a JGI called gene.

K+ transport system, NAD-binding component

2797145..2798779(-)

Potassium channel protein-1

Start 2798779
Stop 2797145
Potassium channel protein-1.png
This is the same as a JGI called gene.

K+ transport system, NAD-binding component

1146592..1148280(-)

NhaP-type Na+(K+)/H+ antiporter

3021102..3022994(+)

Trk system potassium uptake protein trkA-2

Start 3021102
Stop 3022994
Trk system potassium uptake protein-2.png
This is the same as a JGI called gene.

I found no genes with predicted functions that are associated with Cl- from JGI

In RAST, I found seven genes related to potassium homeostasis that were not called in JGI:

Cobalt-zinc-cadmium resistance protein

Start: 2285691
Stop: 2284783
Cobalt-zinc-cadmium resistance protein.png

Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) / Phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3)

Start 678963
Stop 680573
Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2).png

Hydroxyacylglutathione hydrolase (EC 3.1.2.6)-1

Start 2604831
Stop 2605442
Hydroxyacylglutathione hydrolase (EC 3.1.2.6).png

Hydroxyacylglutathione hydrolase (EC 3.1.2.6)-2

Start 1276452
Stop 1277027
Hydroxyacylglutathione hydrolase (EC 3.1.2.6)-2.png

Kef-type K+ transport systems (NAD-binding component fused to domain related to exopolyphosphatase)-1

Start 1431353
Stop 1429968
Potassium transport systems-1.png

Kef-type K+ transport systems (NAD-binding component fused to domain related to exopolyphosphatase)-2

Start 1650228
Stop 1648756
Potassium transport systems-2.png

Potassium channel protein-2

Start 2916660
Stop 2915455
Potassium channel protein-2.png

I found no genes with predicted functions that are associated with Cl- function on RAST.

Are the genes for this process highly conserved among halophiles?

Blast results for JGI genes:

Blastn results for K+ transport system, NAD-binding component
Haloarcula marismortui ATCC 43049 chromosome I, complete sequence
Marismortui 1.png Marismortui 2.png Halobacterium salinarum complete genome, strain R1
Salinarum 1.png Halobacterium sp. NRC-1, complete genome NRC-1.png
Blastn results for K+ transport system, NAD-binding component
Haloarcula marismortui ATCC 43049 chromosome I, complete sequence Marismortui 3.png Marismortui 4.png Halobacterium salinarum complete genome, strain R1 Salinarum 2.png Halobacterium sp. NRC-1, complete genome NRC-1 2.png
Blastn results for K+ transport system, NAD-binding component
Haloarcula marismortui ATCC 43049 chromosome I, complete sequence Marismortui 5.png
Blastn results for Kef-type K+ ransport system, predicted NAD-binding component
Haloarcula marismortui ATCC 43049 chromosome I, complete sequence Marismortui 6.png Marismortui 7.png Halorubrum lacusprofundi ATCC 49239 chromosome 1, complete sequence Lacusprofundi 1.png Lacusprofundi 2.png Halobacterium salinarum complete genome, strain R1 Salinarum 3.png Salinarum 4.png Halobacterium sp. NRC-1, complete genome NRC-1 3.png NRC-1 4.png Natronomonas pharaonis DSM 2160 complete genome Pharaonis 1.png Pharaonis 2.png
Blastn results for Kef-type K+ transport system, membrane component
Halorubrum lacusprofundi ATCC 49239 chromosome 1, complete sequence Lacusprofundi 3.png Lacusprofundi 4.png Haloarcula marismortui ATCC 43049 chromosome I, complete sequence Marismortui 8.png Marismortui 9.png
Blastn results for K+ transport system, NAD-binding component
Halorubrum lacusprofundi ATCC 49239 chromosome 1, complete sequence Lacusprofundi 5.png Lacusprofundi 6.png Natronomonas pharaonis DSM 2160 complete genome Pharaonis 3.png Pharaonis 4.png
Blastn results for Trk-type K+ transport system, membrane component
Natronomonas pharaonis DSM 2160 complete genome Pharaonis 5.png Pharaonis 6.png [Halorubrum lacusprofundi ATCC 49239 chromosome 1, complete sequence http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=BJ9VZPHM01N&log%24=nuclalign&blast_rank=3&list_uids=222451341] Lacusprofundi 7.png Lacusprofundi 8.png Haloarcula marismortui ATCC 43049 chromosome I, complete sequence Marismortui 10.png Marismortui 11.png Halobacterium salinarum PHS3 plasmid complete genome, strain Salinarum 5.png Salinarum 6.png
Blastn results for K+ transport system, NAD-binding component
Haloarcula marismortui ATCC 43049 chromosome I, complete sequence Marismortui 12.png Marismortui 13.png Halobacterium salinarum complete genome, strain R1 Salinarum 7.png Salinarum 8.png Halobacterium sp. NRC-1, complete genome NRC-1 5.png NRC-1 6.png Halorubrum lacusprofundi ATCC 49239 chromosome 1, complete sequence Lacusprofundi 9.png Lacusprofundi 10.png

The blastn results are becoming very repetitive. I think at this point, the way to attack this problem may be to look into this list of 5-6 species that seem to share the potassium proteins seen in our species. If I can find a common thread in how other species are utilizing the same potassium homeostasis machinery, it will tell me a great deal about how our own species is using all these potassium related genes.

It is important to note that many of these genes were also related to the species Halorhabdus utahensis. I did not include the blastn results for this species because Blast could not specify which gene segment these matches were a part of. I believe this was not included simply because this species has not been annotated (or the annotation has not been entered into blast). In any comparison of species that takes place after this, I will need to include this species as well.

Is potassium homeostasis related to our species ability to survive/thrive in high salinity environments? How?

"Cell membranes are freely permeable to water, so the only way to prevent the loss of cellular water under high salt conditions is to increase the internal solute concentration. Halotolerantand halophilic microorganisms therefore accumulate high solute concentrations within the cytoplasm." [1]

I am beginning to understand potassium homeostasis and how it may be useful to our organism to survive in high salt concentrations by first researching how other known species utilize this mechanism. In a paper by Strahl and Greie, the Halobacterium salinarum species use of potassium homeostasis to maintain life in a high salinity environment is described. Apparently these organisms maintain life in such conditions by creating an equimolar condition within their cytoplasm. KCl is the preferred ion to create this equal osmolality for this halobacterium resulting in osmotic equilibrium with the surrounding environment. The K+ ion enters the cell by both passive transport mechanisms as well as active transport mechanisms. A gene, kdpFABC, has been discovered in this organism that codes for homologs of a bacterial ATP-driven K+ uptake system. Deletion of this gene is detrimental to organism survival in limiting K+ conditions. This paper also mentions that this mechanism is unique to this and another species of halobacterium because other halophiles utilize organic solutes to equalize osmotic pressures in high salinity environments. I must determine whether or not potassium homeostasis could be a mechanism of maintaining osmotic equilibrium in our species.

A paper by Oren et al. describes another species, Salinibacter ruber, that appears to be capable of surviving in high salinity environments due to the uptake of high concentrations of potassium. The finding that potassium homeostasis seems to be the mechanism of maintaining life in a high salinity environment was determined by measuring K+, Cl+, glutamate, glycine betaine, and N-alpha-acetyllysine concentrations within the cytoplasm. High amounts of K+ and Cl+ were found within the cytoplasm but low amounts of glutamate, glycine betaine, and N-alpha-acetyllysine were discovered. These three organic solutes are often associated with maintaining osmotic equilibrium in archaic halophiles that exist in high salinity environments. It is unusual that this species does not utilize these organic solutes to maintain homeostasis but instead seems to be utilizing the inorganic molecule KCl. This paper provides another example of potassium concentrations being utilized to maintain life in high salinity environments. I need to determine if our species is using this inorganic molecule or the more common organic molecules to maintain osmotic balance in a high salinity environment.

H. salinarum K+ transport mechanism comparison Found the nucleotide sequence for the KdpFABC operon in the species H. salinarum using NCBI. Compared this sequence to our species genome using Blastx. Found three significant hits:

heavy metal translocating P-type ATPase-1
Heavy metal translocating P-type ATPase-1.png

heavy metal translocating P-type ATPase-2
Heavy metal translocating P-type ATPase-2.png

heavy metal translocating P-type ATPase-3
Heavy metal translocating P-type ATPase-3.png

These hits could just be related to the ATPase function of the Kdp operon in H. salinarum and have nothing to do with potassium transport. I am going to redo this blastx with individual genes from operon Kdp compared to our species genome separately. When blasted separately, I found that the three hits from above were in the gene KdpB in the operon of H salinarum. No other similarities, however, were discovered.

Other species potassium uptake systems For the 6 other species that have similar potassium related genes to our species (Halorhabdus utahensis, Halorubrum lacusprofundi, Halobacterium sp. NRC-1, Haloarcula marismortui, Natronomonas pharaonis, & Halogeometricum borinquense. Excluding Halobacterium salinarum since I already compared the KdpFABC operon), I reviewed literature and did pubmed searches trying to find anything that would relate potassium to these species. The only time I found potassium mentioned in conjunction with one of these species was when one website said that Halobacterium sp. NRC-1 has potassium uptake systems coded for in its genome Kenyon MicrobeWiki. Since this was the only time potassium was mentioned in conjunction with any of these species, it is unlikely that potassium is essential for the survival of these species. Because of this fact and the lack of evidence of the KdpFABC operon in our species genome, it seems unlikely that potassium homeostasis is essential for our species survival in high salinity environments.