TY  - JOUR
AU  - Guzik, Maciej
AU  - Narančić, Tanja
AU  - Ilić-Tomić, Tatjana
AU  - Vojnović, Sandra
AU  - Kenny, Shane T.
AU  - Casey, William T.
AU  - Duane, Gearoid F.
AU  - Casey, Eoin
AU  - Woods, Trevor
AU  - Babu, Ramesh P.
AU  - Nikodinović-Runić, Jasmina
AU  - O'Connor, Kevin E.
PY  - 2014
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/1846
AB  - Diverse and elaborate pathways for nutrient utilization, as well as mechanisms to combat unfavourable nutrient conditions make Pseudomonas putida KT2440 a versatile micro-organism able to occupy a range of ecological niches. The fatty acid degradation pathway of P. putida is complex and correlated with biopolymer medium chain length polyhydroxyalkanoate (mcl-PHA) biosynthesis. Little is known about the second step of fatty acid degradation (beta-oxidation) in this strain. In silico analysis of its genome sequence revealed 21 putative acyl-CoA dehydrogenases (ACADs), four of which were functionally characterized through mutagenesis studies. Four mutants with insertionally inactivated ACADs (PP_1893, PP_2039, PP_2048 and PP_2437) grew and accumulated mcl-PHA on a range of fatty acids as the sole source of carbon and energy. Their ability to grow and accumulate biopolymer was differentially negatively affected on various fatty acids, in comparison to the wild-type strain. Inactive PP_2437 exhibited a pattern of reduced growth and PHA accumulation when fatty acids with lengths of 10 to 14 carbon chains were used as substrates. Recombinant expression and biochemical characterization of the purified protein allowed functional annotation in P. putida KT2440 as an ACAD showing clear preference for dodecanoyl-CoA ester as a substrate and optimum activity at 30 degrees C and pH 6.5-7.
PB  - Soc General Microbiology, Reading
T2  - Microbiology, SGM / Society for General Microbiology
T1  - Identification and characterization of an acyl-CoA dehydrogenase from Pseudomonas putida KT2440 that shows preference towards medium to long chain length fatty acids
VL  - 160
SP  - 1760
EP  - 1771
DO  - 10.1099/mic.0.078758-0
ER  - 

@article{
author = "Guzik, Maciej and Narančić, Tanja and Ilić-Tomić, Tatjana and Vojnović, Sandra and Kenny, Shane T. and Casey, William T. and Duane, Gearoid F. and Casey, Eoin and Woods, Trevor and Babu, Ramesh P. and Nikodinović-Runić, Jasmina and O'Connor, Kevin E.",
year = "2014",
abstract = "Diverse and elaborate pathways for nutrient utilization, as well as mechanisms to combat unfavourable nutrient conditions make Pseudomonas putida KT2440 a versatile micro-organism able to occupy a range of ecological niches. The fatty acid degradation pathway of P. putida is complex and correlated with biopolymer medium chain length polyhydroxyalkanoate (mcl-PHA) biosynthesis. Little is known about the second step of fatty acid degradation (beta-oxidation) in this strain. In silico analysis of its genome sequence revealed 21 putative acyl-CoA dehydrogenases (ACADs), four of which were functionally characterized through mutagenesis studies. Four mutants with insertionally inactivated ACADs (PP_1893, PP_2039, PP_2048 and PP_2437) grew and accumulated mcl-PHA on a range of fatty acids as the sole source of carbon and energy. Their ability to grow and accumulate biopolymer was differentially negatively affected on various fatty acids, in comparison to the wild-type strain. Inactive PP_2437 exhibited a pattern of reduced growth and PHA accumulation when fatty acids with lengths of 10 to 14 carbon chains were used as substrates. Recombinant expression and biochemical characterization of the purified protein allowed functional annotation in P. putida KT2440 as an ACAD showing clear preference for dodecanoyl-CoA ester as a substrate and optimum activity at 30 degrees C and pH 6.5-7.",
publisher = "Soc General Microbiology, Reading",
journal = "Microbiology, SGM / Society for General Microbiology",
title = "Identification and characterization of an acyl-CoA dehydrogenase from Pseudomonas putida KT2440 that shows preference towards medium to long chain length fatty acids",
volume = "160",
pages = "1760-1771",
doi = "10.1099/mic.0.078758-0"
}

Guzik, M., Narančić, T., Ilić-Tomić, T., Vojnović, S., Kenny, S. T., Casey, W. T., Duane, G. F., Casey, E., Woods, T., Babu, R. P., Nikodinović-Runić, J.,& O'Connor, K. E.. (2014). Identification and characterization of an acyl-CoA dehydrogenase from Pseudomonas putida KT2440 that shows preference towards medium to long chain length fatty acids. in Microbiology, SGM / Society for General Microbiology
Soc General Microbiology, Reading., 160, 1760-1771.
https://doi.org/10.1099/mic.0.078758-0

Guzik M, Narančić T, Ilić-Tomić T, Vojnović S, Kenny ST, Casey WT, Duane GF, Casey E, Woods T, Babu RP, Nikodinović-Runić J, O'Connor KE. Identification and characterization of an acyl-CoA dehydrogenase from Pseudomonas putida KT2440 that shows preference towards medium to long chain length fatty acids. in Microbiology, SGM / Society for General Microbiology. 2014;160:1760-1771.
doi:10.1099/mic.0.078758-0 .

Guzik, Maciej, Narančić, Tanja, Ilić-Tomić, Tatjana, Vojnović, Sandra, Kenny, Shane T., Casey, William T., Duane, Gearoid F., Casey, Eoin, Woods, Trevor, Babu, Ramesh P., Nikodinović-Runić, Jasmina, O'Connor, Kevin E., "Identification and characterization of an acyl-CoA dehydrogenase from Pseudomonas putida KT2440 that shows preference towards medium to long chain length fatty acids" in Microbiology, SGM / Society for General Microbiology, 160 (2014):1760-1771,
https://doi.org/10.1099/mic.0.078758-0 . .

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 . .