TY  - JOUR
AU  - Nikodinović-Runić, Jasmina
AU  - Casey, Eoin
AU  - Duane, Gearoid F.
AU  - Mitić, Dragana
AU  - Hume, Aisling R.
AU  - Kenny, Shane T.
AU  - O'Connor, Kevin 
PY  - 2011
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/521
AB  - The improvement and modeling of a process for the supply of the volatile aromatic hydrocarbon, styrene, to a fermentor for increased biomass production of the medium chain length polyhydroxyalkanoate (mcl-PHA) accumulating bacterium Pseudomonas putida CA-3 was investigated. Fed-batch experiments were undertaken using different methods to provide the styrene. Initial experiments where styrene was supplied as a liquid to the bioreactor had detrimental effects on cell growth and inhibited PHA polymer accumulation. By changing the feed of gaseous styrene to liquid styrene through the air sparger a 5.4-fold increase in cell dry-weight was achieved (total of 10.56 g L(-1)) which corresponds to a fourfold improvement in PHA production (3.36 g L(-1)) compared to previous studies performed in our laboratory (0.82 g L(-1)). In addition this final improved feeding strategy reduced the release of styrene from the fermentor 50-fold compared to initial experiments (0.12mL total styrene released per 48 h run). An unstructured kinetic model was developed to describe cell growth along with substrate and oxygen utilization. The formation of dispersed gas (air) and liquid (styrene) phases in the medium and the transfer of styrene between the aqueous and dispersed liquid droplet phases was also modeled. The model provided a detailed description of these phase transitions and helped explain how the feeding strategy led to improved process performance in terms of final biomass levels. It also highlighted the key factors to be considered during further process improvement. Biotechnol. Bioeng. 2011; 108: 2447-2455.
PB  - Wiley-Blackwell, Malden
T2  - Biotechnology and Bioengineering
T1  - Process Analysis of the Conversion of Styrene to Biomass and Medium Chain Length Polyhydroxyalkanoate in a Two-Phase Bioreactor
EP  - 2455
IS  - 10
SP  - 2447
VL  - 108
DO  - 10.1002/bit.23187
ER  - 

@article{
author = "Nikodinović-Runić, Jasmina and Casey, Eoin and Duane, Gearoid F. and Mitić, Dragana and Hume, Aisling R. and Kenny, Shane T. and O'Connor, Kevin ",
year = "2011",
abstract = "The improvement and modeling of a process for the supply of the volatile aromatic hydrocarbon, styrene, to a fermentor for increased biomass production of the medium chain length polyhydroxyalkanoate (mcl-PHA) accumulating bacterium Pseudomonas putida CA-3 was investigated. Fed-batch experiments were undertaken using different methods to provide the styrene. Initial experiments where styrene was supplied as a liquid to the bioreactor had detrimental effects on cell growth and inhibited PHA polymer accumulation. By changing the feed of gaseous styrene to liquid styrene through the air sparger a 5.4-fold increase in cell dry-weight was achieved (total of 10.56 g L(-1)) which corresponds to a fourfold improvement in PHA production (3.36 g L(-1)) compared to previous studies performed in our laboratory (0.82 g L(-1)). In addition this final improved feeding strategy reduced the release of styrene from the fermentor 50-fold compared to initial experiments (0.12mL total styrene released per 48 h run). An unstructured kinetic model was developed to describe cell growth along with substrate and oxygen utilization. The formation of dispersed gas (air) and liquid (styrene) phases in the medium and the transfer of styrene between the aqueous and dispersed liquid droplet phases was also modeled. The model provided a detailed description of these phase transitions and helped explain how the feeding strategy led to improved process performance in terms of final biomass levels. It also highlighted the key factors to be considered during further process improvement. Biotechnol. Bioeng. 2011; 108: 2447-2455.",
publisher = "Wiley-Blackwell, Malden",
journal = "Biotechnology and Bioengineering",
title = "Process Analysis of the Conversion of Styrene to Biomass and Medium Chain Length Polyhydroxyalkanoate in a Two-Phase Bioreactor",
pages = "2455-2447",
number = "10",
volume = "108",
doi = "10.1002/bit.23187"
}

Nikodinović-Runić, J., Casey, E., Duane, G. F., Mitić, D., Hume, A. R., Kenny, S. T.,& O'Connor, K.. (2011). Process Analysis of the Conversion of Styrene to Biomass and Medium Chain Length Polyhydroxyalkanoate in a Two-Phase Bioreactor. in Biotechnology and Bioengineering
Wiley-Blackwell, Malden., 108(10), 2447-2455.
https://doi.org/10.1002/bit.23187

Nikodinović-Runić J, Casey E, Duane GF, Mitić D, Hume AR, Kenny ST, O'Connor K. Process Analysis of the Conversion of Styrene to Biomass and Medium Chain Length Polyhydroxyalkanoate in a Two-Phase Bioreactor. in Biotechnology and Bioengineering. 2011;108(10):2447-2455.
doi:10.1002/bit.23187 .

Nikodinović-Runić, Jasmina, Casey, Eoin, Duane, Gearoid F., Mitić, Dragana, Hume, Aisling R., Kenny, Shane T., O'Connor, Kevin , "Process Analysis of the Conversion of Styrene to Biomass and Medium Chain Length Polyhydroxyalkanoate in a Two-Phase Bioreactor" in Biotechnology and Bioengineering, 108, no. 10 (2011):2447-2455,
https://doi.org/10.1002/bit.23187 . .

TY  - JOUR
AU  - Nikodinović-Runić, Jasmina
AU  - Flanagan, Michelle
AU  - Hume, Aisling R.
AU  - Cagney, Gerard
AU  - O'Connor, Kevin 
PY  - 2009
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/373
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  - Microbiology Soc, London
T2  - Microbiology-Sgm
T1  - Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions
EP  - 3361
SP  - 3348
VL  - 155
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 ",
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 = "Microbiology Soc, London",
journal = "Microbiology-Sgm",
title = "Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions",
pages = "3361-3348",
volume = "155",
doi = "10.1099/mic.0.031153-0"
}

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

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

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

TY  - JOUR
AU  - Hume, Aisling R.
AU  - Nikodinović-Runić, Jasmina
AU  - O'Connor, Kevin 
PY  - 2009
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/377
AB  - A fatty acyl coenzyme A synthetase (FadD) from Pseudomonas putida CA-3 is capable of activating a wide range of phenylalkanoic and alkanoic acids. It exhibits the highest rates of reaction and catalytic efficiency with long-chain aromatic and aliphatic substrates. FadD exhibits higher k(cat) and Km values for aromatic substrates than for the aliphatic equivalents (e. g., 15-phenylpentadecanoic acid versus pentadecanoic acid). FadD is inhibited noncompetitively by both acrylic acid and 2-bromooctanoic acid. The deletion of the fadD gene from P. putida CA-3 resulted in no detectable growth or polyhydroxyalkanoate (PHA) accumulation with 10-phenyldecanoic acid, decanoic acid, and longer-chain substrates. The results suggest that FadD is solely responsible for the activation of long-chain phenylalkanoic and alkanoic acids. While the CA-3 Delta fadD mutant could grow on medium-chain substrates, a decrease in growth yield and PHA accumulation was observed. The PHA accumulated by CA-3 Delta fadD contained a greater proportion of short-chain monomers than did wild-type PHA. Growth of CA-3 Delta fadD was unaffected, but PHA accumulation decreased modestly with shorter-chain substrates. The complemented mutant regained 70% to 90% of the growth and PHA-accumulating ability of the wild-type strain depending on the substrate. The expression of an extra copy of fadD in P. putida CA-3 resulted in increased levels of PHA accumulation (up to 1.6-fold) and an increase in the incorporation of longer-monomer units into the PHA polymer.
PB  - Amer Soc Microbiology, Washington
T2  - Journal of Bacteriology
T1  - FadD from Pseudomonas putida CA-3 Is a True Long-Chain Fatty Acyl Coenzyme A Synthetase That Activates Phenylalkanoic and Alkanoic Acids
EP  - 7565
IS  - 24
SP  - 7554
VL  - 191
DO  - 10.1128/JB.01016-09
ER  - 

@article{
author = "Hume, Aisling R. and Nikodinović-Runić, Jasmina and O'Connor, Kevin ",
year = "2009",
abstract = "A fatty acyl coenzyme A synthetase (FadD) from Pseudomonas putida CA-3 is capable of activating a wide range of phenylalkanoic and alkanoic acids. It exhibits the highest rates of reaction and catalytic efficiency with long-chain aromatic and aliphatic substrates. FadD exhibits higher k(cat) and Km values for aromatic substrates than for the aliphatic equivalents (e. g., 15-phenylpentadecanoic acid versus pentadecanoic acid). FadD is inhibited noncompetitively by both acrylic acid and 2-bromooctanoic acid. The deletion of the fadD gene from P. putida CA-3 resulted in no detectable growth or polyhydroxyalkanoate (PHA) accumulation with 10-phenyldecanoic acid, decanoic acid, and longer-chain substrates. The results suggest that FadD is solely responsible for the activation of long-chain phenylalkanoic and alkanoic acids. While the CA-3 Delta fadD mutant could grow on medium-chain substrates, a decrease in growth yield and PHA accumulation was observed. The PHA accumulated by CA-3 Delta fadD contained a greater proportion of short-chain monomers than did wild-type PHA. Growth of CA-3 Delta fadD was unaffected, but PHA accumulation decreased modestly with shorter-chain substrates. The complemented mutant regained 70% to 90% of the growth and PHA-accumulating ability of the wild-type strain depending on the substrate. The expression of an extra copy of fadD in P. putida CA-3 resulted in increased levels of PHA accumulation (up to 1.6-fold) and an increase in the incorporation of longer-monomer units into the PHA polymer.",
publisher = "Amer Soc Microbiology, Washington",
journal = "Journal of Bacteriology",
title = "FadD from Pseudomonas putida CA-3 Is a True Long-Chain Fatty Acyl Coenzyme A Synthetase That Activates Phenylalkanoic and Alkanoic Acids",
pages = "7565-7554",
number = "24",
volume = "191",
doi = "10.1128/JB.01016-09"
}

Hume, A. R., Nikodinović-Runić, J.,& O'Connor, K.. (2009). FadD from Pseudomonas putida CA-3 Is a True Long-Chain Fatty Acyl Coenzyme A Synthetase That Activates Phenylalkanoic and Alkanoic Acids. in Journal of Bacteriology
Amer Soc Microbiology, Washington., 191(24), 7554-7565.
https://doi.org/10.1128/JB.01016-09

Hume AR, Nikodinović-Runić J, O'Connor K. FadD from Pseudomonas putida CA-3 Is a True Long-Chain Fatty Acyl Coenzyme A Synthetase That Activates Phenylalkanoic and Alkanoic Acids. in Journal of Bacteriology. 2009;191(24):7554-7565.
doi:10.1128/JB.01016-09 .

Hume, Aisling R., Nikodinović-Runić, Jasmina, O'Connor, Kevin , "FadD from Pseudomonas putida CA-3 Is a True Long-Chain Fatty Acyl Coenzyme A Synthetase That Activates Phenylalkanoic and Alkanoic Acids" in Journal of Bacteriology, 191, no. 24 (2009):7554-7565,
https://doi.org/10.1128/JB.01016-09 . .