TY  - JOUR
AU  - Casey, William T.
AU  - Nikodinović-Runić, Jasmina
AU  - Fonseca Garcia, Pilar
AU  - Guzik, Maciej
AU  - McGrath, John W.
AU  - Quinn, John P.
AU  - Cagney, Gerard
AU  - Auxiliadora Prieto, Maria
AU  - O'Connor, Kevin E.
PY  - 2013
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3553
AB  - The primary enzyme involved in polyphosphate (polyP) synthesis, polyP kinase (ppk), has been deleted in Pseudomonas putidaKT2440. This has resulted in a threefold to sixfold reduction in polyhydroxyalkanoate (PHA) accumulation compared with the wild type under conditions of nitrogen limitation, with either temperature or oxidative (H2O2) stress, when grown on glucose. The accumulation of PHA by ppk mutant was the same as the wild type under nitrogen-limiting growth conditions. There was no difference in polyP levels between wild-type and ppk strains under all growth conditions tested. In the ppk mutant proteome, polyP kinase (PPK) was undetectable, but up-regulation of the polyp-associated proteins polyP adenosine triphosphate (ATP)/nicotinamide adenine dinucleotide (NAD) kinase (PpnK), a putative polyP adenosine monophosphate (AMP) phosphotransferase (PP_1752), and exopolyphosphatase was observed. ppk strain exhibited significantly retarded growth with glycerol as carbon and energy source (42h of lag period compared with 24h in wild-type strain) but similar growth to the wild-type strain with glucose. Analysis of gene transcription revealed downregulation of glycerol kinase and the glycerol facilitator respectively. Glycerol kinase protein expression was also downregulated in the ppk mutant. The deletion of ppk did not affect motility but reduced biofilm formation. Thus, the knockout of the ppk gene has resulted in a number of phenotypic changes to the mutant without affecting polyP accumulation.
PB  - Wiley-Blackwell, Hoboken
T2  - Environmental Microbiology Reports
T1  - The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440
VL  - 5
IS  - 5
SP  - 740
EP  - 746
DO  - 10.1111/1758-2229.12076
ER  - 

@article{
author = "Casey, William T. and Nikodinović-Runić, Jasmina and Fonseca Garcia, Pilar and Guzik, Maciej and McGrath, John W. and Quinn, John P. and Cagney, Gerard and Auxiliadora Prieto, Maria and O'Connor, Kevin E.",
year = "2013",
abstract = "The primary enzyme involved in polyphosphate (polyP) synthesis, polyP kinase (ppk), has been deleted in Pseudomonas putidaKT2440. This has resulted in a threefold to sixfold reduction in polyhydroxyalkanoate (PHA) accumulation compared with the wild type under conditions of nitrogen limitation, with either temperature or oxidative (H2O2) stress, when grown on glucose. The accumulation of PHA by ppk mutant was the same as the wild type under nitrogen-limiting growth conditions. There was no difference in polyP levels between wild-type and ppk strains under all growth conditions tested. In the ppk mutant proteome, polyP kinase (PPK) was undetectable, but up-regulation of the polyp-associated proteins polyP adenosine triphosphate (ATP)/nicotinamide adenine dinucleotide (NAD) kinase (PpnK), a putative polyP adenosine monophosphate (AMP) phosphotransferase (PP_1752), and exopolyphosphatase was observed. ppk strain exhibited significantly retarded growth with glycerol as carbon and energy source (42h of lag period compared with 24h in wild-type strain) but similar growth to the wild-type strain with glucose. Analysis of gene transcription revealed downregulation of glycerol kinase and the glycerol facilitator respectively. Glycerol kinase protein expression was also downregulated in the ppk mutant. The deletion of ppk did not affect motility but reduced biofilm formation. Thus, the knockout of the ppk gene has resulted in a number of phenotypic changes to the mutant without affecting polyP accumulation.",
publisher = "Wiley-Blackwell, Hoboken",
journal = "Environmental Microbiology Reports",
title = "The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440",
volume = "5",
number = "5",
pages = "740-746",
doi = "10.1111/1758-2229.12076"
}

Casey, W. T., Nikodinović-Runić, J., Fonseca Garcia, P., Guzik, M., McGrath, J. W., Quinn, J. P., Cagney, G., Auxiliadora Prieto, M.,& O'Connor, K. E.. (2013). The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440. in Environmental Microbiology Reports
Wiley-Blackwell, Hoboken., 5(5), 740-746.
https://doi.org/10.1111/1758-2229.12076

Casey WT, Nikodinović-Runić J, Fonseca Garcia P, Guzik M, McGrath JW, Quinn JP, Cagney G, Auxiliadora Prieto M, O'Connor KE. The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440. in Environmental Microbiology Reports. 2013;5(5):740-746.
doi:10.1111/1758-2229.12076 .

Casey, William T., Nikodinović-Runić, Jasmina, Fonseca Garcia, Pilar, Guzik, Maciej, McGrath, John W., Quinn, John P., Cagney, Gerard, Auxiliadora Prieto, Maria, O'Connor, Kevin E., "The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440" in Environmental Microbiology Reports, 5, no. 5 (2013):740-746,
https://doi.org/10.1111/1758-2229.12076 . .

TY  - DATA
AU  - Casey, William T.
AU  - Nikodinović-Runić, Jasmina
AU  - Fonseca Garcia, Pilar
AU  - Guzik, Maciej
AU  - McGrath, John W.
AU  - Quinn, John P.
AU  - Cagney, Gerard
AU  - Auxiliadora Prieto, Maria
AU  - O'Connor, Kevin E.
PY  - 2013
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3554
PB  - Wiley-Blackwell, Hoboken
T2  - Environmental Microbiology Reports
T1  - Supplementary data for article: Casey, W. T.; Nikodinović-Runić, J.; Fonseca Garcia, P.; Guzik, M. W.; McGrath, J. W.; Quinn, J. P.; Cagney, G.; Auxiliadora Prieto, M.; O’Connor, K. E. The Effect of Polyphosphate Kinase Gene Deletion on Polyhydroxyalkanoate Accumulation and Carbon Metabolism in Pseudomonas Putida KT2440. Environmental Microbiology Reports 2013, 5 (5), 740–746. https://doi.org/10.1111/1758-2229.12076
UR  - https://hdl.handle.net/21.15107/rcub_cherry_3554
ER  - 

@misc{
author = "Casey, William T. and Nikodinović-Runić, Jasmina and Fonseca Garcia, Pilar and Guzik, Maciej and McGrath, John W. and Quinn, John P. and Cagney, Gerard and Auxiliadora Prieto, Maria and O'Connor, Kevin E.",
year = "2013",
publisher = "Wiley-Blackwell, Hoboken",
journal = "Environmental Microbiology Reports",
title = "Supplementary data for article: Casey, W. T.; Nikodinović-Runić, J.; Fonseca Garcia, P.; Guzik, M. W.; McGrath, J. W.; Quinn, J. P.; Cagney, G.; Auxiliadora Prieto, M.; O’Connor, K. E. The Effect of Polyphosphate Kinase Gene Deletion on Polyhydroxyalkanoate Accumulation and Carbon Metabolism in Pseudomonas Putida KT2440. Environmental Microbiology Reports 2013, 5 (5), 740–746. https://doi.org/10.1111/1758-2229.12076",
url = "https://hdl.handle.net/21.15107/rcub_cherry_3554"
}

Casey, W. T., Nikodinović-Runić, J., Fonseca Garcia, P., Guzik, M., McGrath, J. W., Quinn, J. P., Cagney, G., Auxiliadora Prieto, M.,& O'Connor, K. E.. (2013). Supplementary data for article: Casey, W. T.; Nikodinović-Runić, J.; Fonseca Garcia, P.; Guzik, M. W.; McGrath, J. W.; Quinn, J. P.; Cagney, G.; Auxiliadora Prieto, M.; O’Connor, K. E. The Effect of Polyphosphate Kinase Gene Deletion on Polyhydroxyalkanoate Accumulation and Carbon Metabolism in Pseudomonas Putida KT2440. Environmental Microbiology Reports 2013, 5 (5), 740–746. https://doi.org/10.1111/1758-2229.12076. in Environmental Microbiology Reports
Wiley-Blackwell, Hoboken..
https://hdl.handle.net/21.15107/rcub_cherry_3554

Casey WT, Nikodinović-Runić J, Fonseca Garcia P, Guzik M, McGrath JW, Quinn JP, Cagney G, Auxiliadora Prieto M, O'Connor KE. Supplementary data for article: Casey, W. T.; Nikodinović-Runić, J.; Fonseca Garcia, P.; Guzik, M. W.; McGrath, J. W.; Quinn, J. P.; Cagney, G.; Auxiliadora Prieto, M.; O’Connor, K. E. The Effect of Polyphosphate Kinase Gene Deletion on Polyhydroxyalkanoate Accumulation and Carbon Metabolism in Pseudomonas Putida KT2440. Environmental Microbiology Reports 2013, 5 (5), 740–746. https://doi.org/10.1111/1758-2229.12076. in Environmental Microbiology Reports. 2013;.
https://hdl.handle.net/21.15107/rcub_cherry_3554 .

Casey, William T., Nikodinović-Runić, Jasmina, Fonseca Garcia, Pilar, Guzik, Maciej, McGrath, John W., Quinn, John P., Cagney, Gerard, Auxiliadora Prieto, Maria, O'Connor, Kevin E., "Supplementary data for article: Casey, W. T.; Nikodinović-Runić, J.; Fonseca Garcia, P.; Guzik, M. W.; McGrath, J. W.; Quinn, J. P.; Cagney, G.; Auxiliadora Prieto, M.; O’Connor, K. E. The Effect of Polyphosphate Kinase Gene Deletion on Polyhydroxyalkanoate Accumulation and Carbon Metabolism in Pseudomonas Putida KT2440. Environmental Microbiology Reports 2013, 5 (5), 740–746. https://doi.org/10.1111/1758-2229.12076" in Environmental Microbiology Reports (2013),
https://hdl.handle.net/21.15107/rcub_cherry_3554 .

TY  - JOUR
AU  - Casey, William T.
AU  - Nikodinović-Runić, Jasmina
AU  - Fonseca Garcia, Pilar
AU  - Guzik, Maciej
AU  - McGrath, John W.
AU  - Quinn, John P.
AU  - Cagney, Gerard
AU  - Auxiliadora Prieto, Maria
AU  - O'Connor, Kevin E.
PY  - 2013
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/1408
AB  - The primary enzyme involved in polyphosphate (polyP) synthesis, polyP kinase (ppk), has been deleted in Pseudomonas putidaKT2440. This has resulted in a threefold to sixfold reduction in polyhydroxyalkanoate (PHA) accumulation compared with the wild type under conditions of nitrogen limitation, with either temperature or oxidative (H2O2) stress, when grown on glucose. The accumulation of PHA by ppk mutant was the same as the wild type under nitrogen-limiting growth conditions. There was no difference in polyP levels between wild-type and ppk strains under all growth conditions tested. In the ppk mutant proteome, polyP kinase (PPK) was undetectable, but up-regulation of the polyp-associated proteins polyP adenosine triphosphate (ATP)/nicotinamide adenine dinucleotide (NAD) kinase (PpnK), a putative polyP adenosine monophosphate (AMP) phosphotransferase (PP_1752), and exopolyphosphatase was observed. ppk strain exhibited significantly retarded growth with glycerol as carbon and energy source (42h of lag period compared with 24h in wild-type strain) but similar growth to the wild-type strain with glucose. Analysis of gene transcription revealed downregulation of glycerol kinase and the glycerol facilitator respectively. Glycerol kinase protein expression was also downregulated in the ppk mutant. The deletion of ppk did not affect motility but reduced biofilm formation. Thus, the knockout of the ppk gene has resulted in a number of phenotypic changes to the mutant without affecting polyP accumulation.
PB  - Wiley-Blackwell, Hoboken
T2  - Environmental Microbiology Reports
T1  - The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440
VL  - 5
IS  - 5
SP  - 740
EP  - 746
DO  - 10.1111/1758-2229.12076
ER  - 

@article{
author = "Casey, William T. and Nikodinović-Runić, Jasmina and Fonseca Garcia, Pilar and Guzik, Maciej and McGrath, John W. and Quinn, John P. and Cagney, Gerard and Auxiliadora Prieto, Maria and O'Connor, Kevin E.",
year = "2013",
abstract = "The primary enzyme involved in polyphosphate (polyP) synthesis, polyP kinase (ppk), has been deleted in Pseudomonas putidaKT2440. This has resulted in a threefold to sixfold reduction in polyhydroxyalkanoate (PHA) accumulation compared with the wild type under conditions of nitrogen limitation, with either temperature or oxidative (H2O2) stress, when grown on glucose. The accumulation of PHA by ppk mutant was the same as the wild type under nitrogen-limiting growth conditions. There was no difference in polyP levels between wild-type and ppk strains under all growth conditions tested. In the ppk mutant proteome, polyP kinase (PPK) was undetectable, but up-regulation of the polyp-associated proteins polyP adenosine triphosphate (ATP)/nicotinamide adenine dinucleotide (NAD) kinase (PpnK), a putative polyP adenosine monophosphate (AMP) phosphotransferase (PP_1752), and exopolyphosphatase was observed. ppk strain exhibited significantly retarded growth with glycerol as carbon and energy source (42h of lag period compared with 24h in wild-type strain) but similar growth to the wild-type strain with glucose. Analysis of gene transcription revealed downregulation of glycerol kinase and the glycerol facilitator respectively. Glycerol kinase protein expression was also downregulated in the ppk mutant. The deletion of ppk did not affect motility but reduced biofilm formation. Thus, the knockout of the ppk gene has resulted in a number of phenotypic changes to the mutant without affecting polyP accumulation.",
publisher = "Wiley-Blackwell, Hoboken",
journal = "Environmental Microbiology Reports",
title = "The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440",
volume = "5",
number = "5",
pages = "740-746",
doi = "10.1111/1758-2229.12076"
}

Casey, W. T., Nikodinović-Runić, J., Fonseca Garcia, P., Guzik, M., McGrath, J. W., Quinn, J. P., Cagney, G., Auxiliadora Prieto, M.,& O'Connor, K. E.. (2013). The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440. in Environmental Microbiology Reports
Wiley-Blackwell, Hoboken., 5(5), 740-746.
https://doi.org/10.1111/1758-2229.12076

Casey WT, Nikodinović-Runić J, Fonseca Garcia P, Guzik M, McGrath JW, Quinn JP, Cagney G, Auxiliadora Prieto M, O'Connor KE. The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440. in Environmental Microbiology Reports. 2013;5(5):740-746.
doi:10.1111/1758-2229.12076 .

Casey, William T., Nikodinović-Runić, Jasmina, Fonseca Garcia, Pilar, Guzik, Maciej, McGrath, John W., Quinn, John P., Cagney, Gerard, Auxiliadora Prieto, Maria, O'Connor, Kevin E., "The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440" in Environmental Microbiology Reports, 5, no. 5 (2013):740-746,
https://doi.org/10.1111/1758-2229.12076 . .

TY  - JOUR
AU  - Nikodinović-Runić, Jasmina
AU  - Flanagan, Michelle
AU  - Hume, Aisling R.
AU  - Cagney, Gerard
AU  - O'Connor, Kevin E.
PY  - 2009
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/1022
AB  - Pseudomonas putida CA-3 is a styrene-degrading bacterium capable of accumulating medium-chain-length polyhydroxyalkanoate (mcIPHA) when exposed to limiting concentrations of a nitrogen source in the growth medium. Using shotgun proteomics we analysed global proteome expression in P. putida CA-3 supplied with styrene as the sole carbon and energy source under N-limiting (condition permissive for mclPHA synthesis) and non-limiting (condition non-permissive for mcIPHA accumulation) growth conditions in order to provide insight into the molecular response of P. putida CA-3 to limitation of nitrogen when grown on styrene. A total of 1761 proteins were identified with high confidence and the detected proteins could be assigned to functional groups including styrene degradation, energy, nucleotide metabolism, protein synthesis, transport, stress response and motility. Proteins involved in the upper and lower styrene degradation pathway were expressed throughout the 48 h growth period under both nitrogen limitation and excess. Proteins involved in polyhydroxyalkanoate (PHA) biosynthesis, nitrogen assimilation and amino acid transport, and outer membrane proteins were upregulated under nitrogen limitation. PHA accumulation and biosynthesis were only expressed under nitrogen limitation. Nitrogen assimilation proteins were detected on average at twofold higher amounts under nitrogen limitation. Expression of the branched-chain amino acid ABC transporter was up to 16-fold higher under nitrogen-limiting conditions. Branched chain amino acid uptake by nitrogen-limited cultures was also higher than that by non-limited cultures. Outer membrane lipoproteins were expressed at twofold higher levels under nitrogen limitation. This was confirmed by Western blotting (immunochemical detection) of cells grown under nitrogen limitation. Our study provides the first global description of protein expression changes during growth of any organism on styrene and accumulating mcIPHA (nitrogen-limited growth).
PB  - Soc General Microbiology, Reading
T2  - Microbiology, SGM / Society for General Microbiology
T1  - Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions
VL  - 155
SP  - 3348
EP  - 3361
DO  - 10.1099/mic.0.031153-0
ER  - 

@article{
author = "Nikodinović-Runić, Jasmina and Flanagan, Michelle and Hume, Aisling R. and Cagney, Gerard and O'Connor, Kevin E.",
year = "2009",
abstract = "Pseudomonas putida CA-3 is a styrene-degrading bacterium capable of accumulating medium-chain-length polyhydroxyalkanoate (mcIPHA) when exposed to limiting concentrations of a nitrogen source in the growth medium. Using shotgun proteomics we analysed global proteome expression in P. putida CA-3 supplied with styrene as the sole carbon and energy source under N-limiting (condition permissive for mclPHA synthesis) and non-limiting (condition non-permissive for mcIPHA accumulation) growth conditions in order to provide insight into the molecular response of P. putida CA-3 to limitation of nitrogen when grown on styrene. A total of 1761 proteins were identified with high confidence and the detected proteins could be assigned to functional groups including styrene degradation, energy, nucleotide metabolism, protein synthesis, transport, stress response and motility. Proteins involved in the upper and lower styrene degradation pathway were expressed throughout the 48 h growth period under both nitrogen limitation and excess. Proteins involved in polyhydroxyalkanoate (PHA) biosynthesis, nitrogen assimilation and amino acid transport, and outer membrane proteins were upregulated under nitrogen limitation. PHA accumulation and biosynthesis were only expressed under nitrogen limitation. Nitrogen assimilation proteins were detected on average at twofold higher amounts under nitrogen limitation. Expression of the branched-chain amino acid ABC transporter was up to 16-fold higher under nitrogen-limiting conditions. Branched chain amino acid uptake by nitrogen-limited cultures was also higher than that by non-limited cultures. Outer membrane lipoproteins were expressed at twofold higher levels under nitrogen limitation. This was confirmed by Western blotting (immunochemical detection) of cells grown under nitrogen limitation. Our study provides the first global description of protein expression changes during growth of any organism on styrene and accumulating mcIPHA (nitrogen-limited growth).",
publisher = "Soc General Microbiology, Reading",
journal = "Microbiology, SGM / Society for General Microbiology",
title = "Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions",
volume = "155",
pages = "3348-3361",
doi = "10.1099/mic.0.031153-0"
}

Nikodinović-Runić, J., Flanagan, M., Hume, A. R., Cagney, G.,& O'Connor, K. E.. (2009). Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions. in Microbiology, SGM / Society for General Microbiology
Soc General Microbiology, Reading., 155, 3348-3361.
https://doi.org/10.1099/mic.0.031153-0

Nikodinović-Runić J, Flanagan M, Hume AR, Cagney G, O'Connor KE. Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions. in Microbiology, SGM / Society for General Microbiology. 2009;155:3348-3361.
doi:10.1099/mic.0.031153-0 .

Nikodinović-Runić, Jasmina, Flanagan, Michelle, Hume, Aisling R., Cagney, Gerard, O'Connor, Kevin E., "Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions" in Microbiology, SGM / Society for General Microbiology, 155 (2009):3348-3361,
https://doi.org/10.1099/mic.0.031153-0 . .