Difference between revisions of "Prochloron didemni"

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''Prochloron Didemni''
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''Prochloron didemni''
  
 
==Description and significance==
 
==Description and significance==
Prochloron Didemni is a photosynthetic bacteria that lives in symbiosis with the ascidian Lissoclinum patella
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''Prochloron didemni'' is a unicellular cyanobacteria that is photosynthetic and oxygenic. It is an obligate symbiont that lives in the ascidian ''Lissoclinum patella'' and can be found in marine environments.
  
Describe the appearance, habitat, etc. of the organism, and why it is important enough to have its genome sequenced.  Describe how and where it was isolated.
+
The study of ''Prochloron didemni'' and its genome can provide us with valuable information. The genome of ''P. didemni'' is currently incomplete. However, when completed, the genome can be used for analysis to elucidate other genes responsible for symbiosis between bacteria and chordates, such as humans. Also, as a oxygenic, photosynthetic cyanobacteria, ''P. didemni'' is a significant player in global carbon fixation. The study of its metabolic pathways and unique photosynthetic processes would yield information beneficial to biotechnology.
Include a picture or two (with sources) if you can find them.
+
 
 +
R.A. Lewin first discovered ''Prochloron didemni'' in 1975, but identified it as ''Synechocystis didemni''.  In 1977, the presence of chlorophyll a/b and the lack of phycobilins caused it to be transfered to a new genus, ''Prochloron'', and named ''Prochloron didemni''.(4)
  
 
==Genome structure==
 
==Genome structure==
Describe the size and content of the genome. How many chromosomes?  Circular or linear?  Other interesting features?  What is known about its sequence?
+
The complete genome for ''Prochloron didemni'' has not been sequenced but is estimated to be approximately 5 million base pairs long with a molecular weight of 3.59x10^9 daltons.(8,10) This estimate was reached by assembly of 82,337 shotgun reads and Glimmer, a gene-finding software.(10) Denaturation kinetics revealed a Tm of 70.6°C, indicating a GC composition of 40.8 mol%.(8)
Does it have any plasmids?  Are they important to the organism's lifestyle?
+
 
 +
''P. didemni'' possesses homologs to genes ''gap2'' and ''gap3'', glyceraldehyde-3-phosphate dehydrogenase genes, from ''Anabaena''. These genes are needed to produce GADPH, which is used in the Calvin cycle to metabolize carbon.(6) Genes ''patA-patG'' have also been identified, which code for the machinery necessary for patellamide biosynthesis.(1)
  
 
==Cell structure and metabolism==
 
==Cell structure and metabolism==
Describe any interesting features and/or cell structures; how it gains energy; what important molecules it produces.
+
''Prochloron didemni'' are photosynthetic cyanobacteria with a twist. They carry out photosynthesis similar to eukaryotic plants, with two reaction centers in noncyclic electron flow.(7) However, unlike cyanobacteria, ''P. didemni'' have chlorophyll a and b and lack phycobiliprotiens.(2) Photosynthesis takes place in the thylakoids, with the thylakoids concentrated toward the periphery of the cell.(7)
 +
 
 +
The cell wall of ''Prochloron didemni'' consists of peptidoglycan and muramic acid of the A1 γ type. Approximately 40% cross-linkage exists in its cell wall with a network of five to eight layers and a thickness of 12nm.(9)
  
 
==Ecology==
 
==Ecology==
Describe any interactions with other organisms (included eukaryotes), contributions to the environment, effect on environment, etc.
+
''Prochloron didemni'' is an obligate symbiont that lives in the ascidian ''Lissoclinum patella''. ''L. patella'' along with ''P. didemni'' can be found in tropical waters, such as the reefs in Hawaii and the Great Barrier Reef in Australia.(2,7)
  
==Pathology==
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Exchange of nutrients is the main reason for the symbiotic relationship between ''L. patella'' and ''P. didemni''. Photosynthesis by ''P. didemni'' provides 60-100% of the organic carbon needed by ''L. patella''. There is also evidence that suggests there is nitrogen cycling between the host and symbiont as well as nitrogen fixation. In exchange for the organic carbons and nitrogen cycling, ''L. patella'' provides optimal growth conditions by moving to areas with proper sunlight and a tunic covering.(1)
How does this organism cause disease?  Human, animal, plant hosts?  Virulence factors, as well as patient symptoms.
+
 
 +
Patellamides, a product of ''P. didemni'', also play in role in the symbiosis. The cytotoxic characteristic of patellamides may be used as feeding deterrents and patellamides' ability to chelate metals, such as copper and zinc, may be used in detoxification.(1)
  
 
==Application to Biotechnology==
 
==Application to Biotechnology==
Does this organism produce any useful compounds or enzymes? What are they and how are they used?
+
One of the major problems with treating cancer is multi drug resistance. A recent study on ''Prochloron didemni'' revealed that it produces Patellamides A and C, which can be used to reverse multi drug resistance in cancer cells.(1)  
 +
 
 +
Patellamides are psuedosymmetrical, cyclic dimers. Each substructure of patellamide contains the specific sequence thiazole-nonpolar amino acid-oxazoline-nonpolar amino acid. Study show that patellamides A and C are ribosomally synthesized and encoded on a single ORF. Genes ''patA - patG'' are responsible for the biosynthesis of patellamides. It is currently known that ''patA'' codes for a Subtilisin-like protease, ''patD'' for an adenylating enzyme-hydrolase hybrid, ''patE'' the precursor peptide, and ''patG'' a oxidoreductase-protease hybrid. Functions of ''patB,C,& F'' are still unknown.(1)
  
 
==Current Research==
 
==Current Research==
 +
===Anti-Cancer Compound===
 +
A promising study showed that patellamides, a product of ''Prochloron didemni'' that can reverse multi drug resistance, can be synthesized by transfer of a biosynthetic pathway. Because ''P. didemni'' is an obligate symbiont, it could not be cultivated. To bypass this problem, the genes responsible for patellamide biosynthesis were identified, cloned, and expressed in ''E.Coli''.(1)
 +
 +
Searching for a nonribosomal peptide synthetase (NRPS) adenylation domain yielded a single gene, ''prnA''. Further analysis revealed that this was the wrong domain architecture for patellamide biosynthesis. This pointed to ribosomal synthesis of patellamides. A TBLASTN search lead to ''patE'', the gene for the patellamide precursor peptide. Surrounding ''patE'' were other genes necessary for patellamide biosynthesis, ranging form ''patA'' tot ''patG''. ''patA'' codes for a protease, ''patD'' a adenylating enzyme-hydrolase hybrid, and ''patG'' a oxidoreductase-protease hybrid. The functions of ''patB, patC,'' and ''patF'' are still unknown.(1)
  
Enter summaries of the most recent research here--at least three required
+
Further study of the genome of ''P. didemni'' will continue to reveal genes involved in patellamide production as well as symbiotic mechanisms and pathways.
 +
 
 +
===Isolation of Photosystem II Supercomplex===
 +
It was recently shown that ''Prochlorococcus marinus'' SS120 had a 18-Pcb subunit, light-harvesting antenna ring around photosystem I. Investigation of ''Prochloron didemni'' revealed that it had a similar supercomplex around photosystem II. The supercomplex is a photosystem II core dimer with five Pcb proteins on each side. Assuming that photosystem II core monomer binds 35 chlorophylls and each Pcb protein, like CP43, binds 13 chlorophylls, the supercomplex would increase the light-harvesting capacity of by ~200%. This increase in absorption power compensates for the lack of phycobiliproteins.(2)
 +
 
 +
===Isolation of Thylakoids===
 +
Oxygen evolving thylakoids and membrane fragments were isolated from ''Prochloron didemni'' to investigate structural and functional conservation of oxyphotosynthetic processes. ''P. didemni'' cells were suspended in four different isolation buffers, including buffered seawater. Suspension in different buffers yielded constant Fv/Fm ratios but varying electron transfer rates (ETR). Suspension of ''P.didemni'' cells in isoosmolar aqueous buffers caused deletrious effects within five minutes and could not be reversed by resuspension in seawater. This indicates that oxygen evolution is inhibited due to diffusive loss of components necessary to maintain ETR and exchange between the cell and the environment. Further confirmation was achieved when the addition of artificial acceptors (ie. PPBQ) resulted in increased ETR.(5)
 +
 
 +
To isolate thylakoids and thylakoid membrane fragments, the Yeda press treatment was utilized followed by differential centrifugation. The cells suspended in seawater had more than 80% of the chlorophyll concentration in the thylakoid and thylakoid membrane fraction. For this reason, only the seawater samples were used. Using detergents, such as Triton X-100 and digitonin, to isolate thylakoids and thylakoid membranes was unsuccessful. Analysis of the P680+ from the isolated samples revealed similarities between ''P.didemni'' and other cyanobacteria and higher plants. The results of the study provided evidence that the "inner core" of photosystem II was conserved while regulating subunits underwent significant changes during the evolution of oxygen evolving organisms.(5)
  
 
==References==
 
==References==
[Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "''Palaeococcus ferrophilus'' gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". ''International Journal of Systematic and Evolutionary Microbiology''. 2000. Volume 50. p. 489-500.]
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(1) [http://www.pnas.org/cgi/doi/10.1073/pnas.0501424102 Schmidt, E., Nelson, J., Rasko, D., Sudek, S., Eisen, J., Haygood, M., and Ravel, J. "Patellamide A and C biosynthesis by a microcin-like pathway in ''Prochloron didemni'', the cyanobacterial symbiont of ''Lissoclinum patella''". ''PNAS''. May, 17, 2005. Volume 102. No. 20 p. 7315-7320.]
 +
 
 +
(2) [http://www.pnas.org/cgi/doi/10.1073/pnas.1532271100 Bibby, T., Nield, J., Chen, M., Larkum, A., and Barber, J. "Structure of a photosystem II supercomplex isolated from ''Prochloron didemni'' retaining its chlorophyll a/b light-harvesting system". ''PNAS''. July, 22, 2003. Volume 100. No. 15 p. 9050-9054.]
 +
 
 +
(3) Lockhart, P., Beanland, T., Howe, C., and Larkum, A. "Sequence of ''Prochloron didemni atpBE'' and the inference of chloroplast origins". ''Proc. Natl. Acad. Sci. USA: Evolution''. April, 1992. Volume 89. p. 2742-2746.]
 +
 
 +
(4) [http://links.jstor.org/sici?sici=0040-0262%28199308%2942%3A3%3C641%3AVOPD%28A%3E2.0.CO%3B2-Y Hoffman, L., and Greuter, W. "Validation of ''Prochloron didemni'' (Cyanophyta and Nomenclatural Discussion of Correlated Names at the Higher Ranks". ''Taxon''. August, 1993. Volume 42. No. 3 p. 641-645.]
 +
 
 +
(5) Christen, G., Stevens, G., Lukins, P., Renger, G., and Larkum, A. "Isolation and characterisation of oxygen evolving thylakoids from the marine prokaryote ''Prochloron didemni''". ''FEBS''. March, 1999. Letters 449 p. 264-268.
 +
 
 +
(6) Figge, R., Schubert, M., Brinkmann, H., and Cerff, R. "Glyceraldehyde-3-Phosphate Dehydrogenase Gene Diversity in Eubacteria and Eukaryotes: Evidence for Intra- and Inter-Kingdom Gene Transfer". ''Mol. Biol. Evol.''. 1999. p. 429-440.
 +
 
 +
(7) Giddings Jr., T., Withers, N., and Staehelin, L. A. "Supramolecular structure of stacked and unstacked regions of the photosynthetic membranes of ''Prochloron'' sp., a prokaryote". ''Proc. Natl. Acad. Sci. USA: Botany''. January, 1980. Volume 77. No. 1 p. 352-356.
 +
 
 +
(8) Herdman, M. "Deoxyribonucleic Acid Base Composition and Genome Size of ''Prochloron''". ''Arch Microbiol''. 1981. Volume 129. p. 314-316.
 +
 
 +
(9) Jurgens, U., Burger-Wiersma, T. "Peptidoglycan-Polysaccharide Complex in the Cell Wall of the Filamentous Prochlorophyte ''Prochlorothrix hollandica''". ''Journal of Bacteriology''. January, 1989. Volume 171. No. 1 p. 498-502.
 +
 
 +
(10) Delcher, A., Bratke, K., Powers, E., and Salzberg, S. "Identifying bacterial genes and endosymbiont DNA with Glimmer" ''Bioinformatics''. January, 2007. Volume 23. No. 6 p. 673-679.
  
 
Edited by Edward Lee [mailto:etlee81@gmail.com Eddie Lee], a student of Rachel Larsen [mailto:ralarsen@ucsd.edu Rachel Larsen]
 
Edited by Edward Lee [mailto:etlee81@gmail.com Eddie Lee], a student of Rachel Larsen [mailto:ralarsen@ucsd.edu Rachel Larsen]
 +
 +
Edited by KLB

Latest revision as of 03:29, 20 August 2010

This student page has not been curated.

A Microbial Biorealm page on the genus Prochloron didemni

Classification

Higher order taxa

Cellular Organisms; Bacteria; Cyanobacteria; Prochlorales; Prochloraceae; Prochloron

Species

NCBI: Taxonomy

Prochloron didemni

Description and significance

Prochloron didemni is a unicellular cyanobacteria that is photosynthetic and oxygenic. It is an obligate symbiont that lives in the ascidian Lissoclinum patella and can be found in marine environments.

The study of Prochloron didemni and its genome can provide us with valuable information. The genome of P. didemni is currently incomplete. However, when completed, the genome can be used for analysis to elucidate other genes responsible for symbiosis between bacteria and chordates, such as humans. Also, as a oxygenic, photosynthetic cyanobacteria, P. didemni is a significant player in global carbon fixation. The study of its metabolic pathways and unique photosynthetic processes would yield information beneficial to biotechnology.

R.A. Lewin first discovered Prochloron didemni in 1975, but identified it as Synechocystis didemni. In 1977, the presence of chlorophyll a/b and the lack of phycobilins caused it to be transfered to a new genus, Prochloron, and named Prochloron didemni.(4)

Genome structure

The complete genome for Prochloron didemni has not been sequenced but is estimated to be approximately 5 million base pairs long with a molecular weight of 3.59x10^9 daltons.(8,10) This estimate was reached by assembly of 82,337 shotgun reads and Glimmer, a gene-finding software.(10) Denaturation kinetics revealed a Tm of 70.6°C, indicating a GC composition of 40.8 mol%.(8)

P. didemni possesses homologs to genes gap2 and gap3, glyceraldehyde-3-phosphate dehydrogenase genes, from Anabaena. These genes are needed to produce GADPH, which is used in the Calvin cycle to metabolize carbon.(6) Genes patA-patG have also been identified, which code for the machinery necessary for patellamide biosynthesis.(1)

Cell structure and metabolism

Prochloron didemni are photosynthetic cyanobacteria with a twist. They carry out photosynthesis similar to eukaryotic plants, with two reaction centers in noncyclic electron flow.(7) However, unlike cyanobacteria, P. didemni have chlorophyll a and b and lack phycobiliprotiens.(2) Photosynthesis takes place in the thylakoids, with the thylakoids concentrated toward the periphery of the cell.(7)

The cell wall of Prochloron didemni consists of peptidoglycan and muramic acid of the A1 γ type. Approximately 40% cross-linkage exists in its cell wall with a network of five to eight layers and a thickness of 12nm.(9)

Ecology

Prochloron didemni is an obligate symbiont that lives in the ascidian Lissoclinum patella. L. patella along with P. didemni can be found in tropical waters, such as the reefs in Hawaii and the Great Barrier Reef in Australia.(2,7)

Exchange of nutrients is the main reason for the symbiotic relationship between L. patella and P. didemni. Photosynthesis by P. didemni provides 60-100% of the organic carbon needed by L. patella. There is also evidence that suggests there is nitrogen cycling between the host and symbiont as well as nitrogen fixation. In exchange for the organic carbons and nitrogen cycling, L. patella provides optimal growth conditions by moving to areas with proper sunlight and a tunic covering.(1)

Patellamides, a product of P. didemni, also play in role in the symbiosis. The cytotoxic characteristic of patellamides may be used as feeding deterrents and patellamides' ability to chelate metals, such as copper and zinc, may be used in detoxification.(1)

Application to Biotechnology

One of the major problems with treating cancer is multi drug resistance. A recent study on Prochloron didemni revealed that it produces Patellamides A and C, which can be used to reverse multi drug resistance in cancer cells.(1)

Patellamides are psuedosymmetrical, cyclic dimers. Each substructure of patellamide contains the specific sequence thiazole-nonpolar amino acid-oxazoline-nonpolar amino acid. Study show that patellamides A and C are ribosomally synthesized and encoded on a single ORF. Genes patA - patG are responsible for the biosynthesis of patellamides. It is currently known that patA codes for a Subtilisin-like protease, patD for an adenylating enzyme-hydrolase hybrid, patE the precursor peptide, and patG a oxidoreductase-protease hybrid. Functions of patB,C,& F are still unknown.(1)

Current Research

Anti-Cancer Compound

A promising study showed that patellamides, a product of Prochloron didemni that can reverse multi drug resistance, can be synthesized by transfer of a biosynthetic pathway. Because P. didemni is an obligate symbiont, it could not be cultivated. To bypass this problem, the genes responsible for patellamide biosynthesis were identified, cloned, and expressed in E.Coli.(1)

Searching for a nonribosomal peptide synthetase (NRPS) adenylation domain yielded a single gene, prnA. Further analysis revealed that this was the wrong domain architecture for patellamide biosynthesis. This pointed to ribosomal synthesis of patellamides. A TBLASTN search lead to patE, the gene for the patellamide precursor peptide. Surrounding patE were other genes necessary for patellamide biosynthesis, ranging form patA tot patG. patA codes for a protease, patD a adenylating enzyme-hydrolase hybrid, and patG a oxidoreductase-protease hybrid. The functions of patB, patC, and patF are still unknown.(1)

Further study of the genome of P. didemni will continue to reveal genes involved in patellamide production as well as symbiotic mechanisms and pathways.

Isolation of Photosystem II Supercomplex

It was recently shown that Prochlorococcus marinus SS120 had a 18-Pcb subunit, light-harvesting antenna ring around photosystem I. Investigation of Prochloron didemni revealed that it had a similar supercomplex around photosystem II. The supercomplex is a photosystem II core dimer with five Pcb proteins on each side. Assuming that photosystem II core monomer binds 35 chlorophylls and each Pcb protein, like CP43, binds 13 chlorophylls, the supercomplex would increase the light-harvesting capacity of by ~200%. This increase in absorption power compensates for the lack of phycobiliproteins.(2)

Isolation of Thylakoids

Oxygen evolving thylakoids and membrane fragments were isolated from Prochloron didemni to investigate structural and functional conservation of oxyphotosynthetic processes. P. didemni cells were suspended in four different isolation buffers, including buffered seawater. Suspension in different buffers yielded constant Fv/Fm ratios but varying electron transfer rates (ETR). Suspension of P.didemni cells in isoosmolar aqueous buffers caused deletrious effects within five minutes and could not be reversed by resuspension in seawater. This indicates that oxygen evolution is inhibited due to diffusive loss of components necessary to maintain ETR and exchange between the cell and the environment. Further confirmation was achieved when the addition of artificial acceptors (ie. PPBQ) resulted in increased ETR.(5)

To isolate thylakoids and thylakoid membrane fragments, the Yeda press treatment was utilized followed by differential centrifugation. The cells suspended in seawater had more than 80% of the chlorophyll concentration in the thylakoid and thylakoid membrane fraction. For this reason, only the seawater samples were used. Using detergents, such as Triton X-100 and digitonin, to isolate thylakoids and thylakoid membranes was unsuccessful. Analysis of the P680+ from the isolated samples revealed similarities between P.didemni and other cyanobacteria and higher plants. The results of the study provided evidence that the "inner core" of photosystem II was conserved while regulating subunits underwent significant changes during the evolution of oxygen evolving organisms.(5)

References

(1) Schmidt, E., Nelson, J., Rasko, D., Sudek, S., Eisen, J., Haygood, M., and Ravel, J. "Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella". PNAS. May, 17, 2005. Volume 102. No. 20 p. 7315-7320.

(2) Bibby, T., Nield, J., Chen, M., Larkum, A., and Barber, J. "Structure of a photosystem II supercomplex isolated from Prochloron didemni retaining its chlorophyll a/b light-harvesting system". PNAS. July, 22, 2003. Volume 100. No. 15 p. 9050-9054.

(3) Lockhart, P., Beanland, T., Howe, C., and Larkum, A. "Sequence of Prochloron didemni atpBE and the inference of chloroplast origins". Proc. Natl. Acad. Sci. USA: Evolution. April, 1992. Volume 89. p. 2742-2746.]

(4) Hoffman, L., and Greuter, W. "Validation of Prochloron didemni (Cyanophyta and Nomenclatural Discussion of Correlated Names at the Higher Ranks". Taxon. August, 1993. Volume 42. No. 3 p. 641-645.

(5) Christen, G., Stevens, G., Lukins, P., Renger, G., and Larkum, A. "Isolation and characterisation of oxygen evolving thylakoids from the marine prokaryote Prochloron didemni". FEBS. March, 1999. Letters 449 p. 264-268.

(6) Figge, R., Schubert, M., Brinkmann, H., and Cerff, R. "Glyceraldehyde-3-Phosphate Dehydrogenase Gene Diversity in Eubacteria and Eukaryotes: Evidence for Intra- and Inter-Kingdom Gene Transfer". Mol. Biol. Evol.. 1999. p. 429-440.

(7) Giddings Jr., T., Withers, N., and Staehelin, L. A. "Supramolecular structure of stacked and unstacked regions of the photosynthetic membranes of Prochloron sp., a prokaryote". Proc. Natl. Acad. Sci. USA: Botany. January, 1980. Volume 77. No. 1 p. 352-356.

(8) Herdman, M. "Deoxyribonucleic Acid Base Composition and Genome Size of Prochloron". Arch Microbiol. 1981. Volume 129. p. 314-316.

(9) Jurgens, U., Burger-Wiersma, T. "Peptidoglycan-Polysaccharide Complex in the Cell Wall of the Filamentous Prochlorophyte Prochlorothrix hollandica". Journal of Bacteriology. January, 1989. Volume 171. No. 1 p. 498-502.

(10) Delcher, A., Bratke, K., Powers, E., and Salzberg, S. "Identifying bacterial genes and endosymbiont DNA with Glimmer" Bioinformatics. January, 2007. Volume 23. No. 6 p. 673-679.

Edited by Edward Lee Eddie Lee, a student of Rachel Larsen Rachel Larsen

Edited by KLB