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Zhou Y, Zhang X, Yu W, Fu Y, Ni L, Yu J, Wang X, Song W, Wang C. Enhancing Pseudomonas cell growth for the production of medium-chain-length polyhydroxyalkanoates from Antarctic krill shell waste. Int J Biol Macromol 2024; 277:133364. [PMID: 38917919 DOI: 10.1016/j.ijbiomac.2024.133364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/10/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024]
Abstract
Antarctic krill shell waste (AKSW), a byproduct of Antarctic krill processing, has substantial quantity but low utilization. Utilizing microbial-based cell factories, with Pseudomonas putida as a promising candidate, offers an ecofriendly and sustainable approach to producing valuable bioproducts from renewable sources. However, the high fluoride content in AKSW impedes the cell growth of P. putida. This study aims to investigate the transcriptional response of P. putida to fluoride stress from AKSW and subsequently conduct genetic modification of the strain based on insights gained from transcriptomic analysis. Notably, the engineered strain KT+16840+03100 exhibited a remarkable 33.7-fold increase in cell growth, capable of fermenting AKSW for medium-chain-length-polyhydroxyalkanoates (mcl-PHA) biosynthesis, achieving a 40.3-fold increase in mcl-PHA yield compared to the control strain. This research advances our understanding of how P. putida responds to fluoride stress from AKSW and provides engineered strains that serve as excellent platforms for producing mcl-PHA through AKSW.
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Affiliation(s)
- Yueyue Zhou
- Marine Economic Research Center, Donghai Academy, Ningbo University, Ningbo 315000, China; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo 315000, China; Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo 315000, China.
| | - Xingyu Zhang
- Marine Economic Research Center, Donghai Academy, Ningbo University, Ningbo 315000, China; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo 315000, China; Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo 315000, China
| | - Wenying Yu
- Ningbo Institute of Oceanography, Ningbo, Zhejiang, China
| | - Yuanyuan Fu
- Ningbo Institute of Oceanography, Ningbo, Zhejiang, China
| | - Lijuan Ni
- Marine Economic Research Center, Donghai Academy, Ningbo University, Ningbo 315000, China
| | - Jiayi Yu
- Marine Economic Research Center, Donghai Academy, Ningbo University, Ningbo 315000, China
| | - Xiaopeng Wang
- Marine Economic Research Center, Donghai Academy, Ningbo University, Ningbo 315000, China; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo 315000, China; Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo 315000, China.
| | - Weiwei Song
- Marine Economic Research Center, Donghai Academy, Ningbo University, Ningbo 315000, China; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo 315000, China; Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo 315000, China.
| | - Chunlin Wang
- Marine Economic Research Center, Donghai Academy, Ningbo University, Ningbo 315000, China; Key Laboratory of Green Mariculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural, Ningbo 315000, China; Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo 315000, China.
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Kelly S, Tham JL, McKeever K, Dillon E, O'Connell D, Scholz D, Simpson JC, O'Connor K, Narancic T, Cagney G. Comprehensive Proteomics Analysis of Polyhydroxyalkanoate (PHA) Biology in Pseudomonas putida KT2440: The Outer Membrane Lipoprotein OprL is a Newly Identified Phasin. Mol Cell Proteomics 2024; 23:100765. [PMID: 38608840 PMCID: PMC11103573 DOI: 10.1016/j.mcpro.2024.100765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/01/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
Pseudomonas putida KT2440 is an important bioplastic-producing industrial microorganism capable of synthesizing the polymeric carbon-rich storage material, polyhydroxyalkanoate (PHA). PHA is sequestered in discrete PHA granules, or carbonosomes, and accumulates under conditions of stress, for example, low levels of available nitrogen. The pha locus responsible for PHA metabolism encodes both anabolic and catabolic enzymes, a transcription factor, and carbonosome-localized proteins termed phasins. The functions of phasins are incompletely understood but genetic disruption of their function causes PHA-related phenotypes. To improve our understanding of these proteins, we investigated the PHA pathways of P.putida KT2440 using three types of experiments. First, we profiled cells grown in nitrogen-limited and nitrogen-excess media using global expression proteomics, identifying sets of proteins found to coordinately increase or decrease within clustered pathways. Next, we analyzed the protein composition of isolated carbonosomes, identifying two new putative components. We carried out physical interaction screens focused on PHA-related proteins, generating a protein-protein network comprising 434 connected proteins. Finally, we confirmed that the outer membrane protein OprL (the Pal component of the Pal-Tol system) localizes to the carbonosome and shows a PHA-related phenotype and therefore is a novel phasin. The combined datasets represent a valuable overview of the protein components of the PHA system in P.putida highlighting the complex nature of regulatory interactions responsive to nutrient stress.
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Affiliation(s)
- Siobhan Kelly
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Jia-Lynn Tham
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Kate McKeever
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Eugene Dillon
- UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - David O'Connell
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Dimitri Scholz
- UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Jeremy C Simpson
- UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; UCD Earth Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Kevin O'Connor
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland; UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Tanja Narancic
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland.
| | - Gerard Cagney
- BiOrbic - Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland; UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland; School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland.
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Fenibo EO, Selvarajan R, Abia ALK, Matambo T. Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162951. [PMID: 36948313 DOI: 10.1016/j.scitotenv.2023.162951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 05/06/2023]
Abstract
Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Akebe Luther King Abia
- Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa; Environmental Research Foundation, Westville 3630, South Africa
| | - Tonderayi Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort 1709, South Africa.
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Nawaz MZ, Shang H, Sun J, Geng A, Ali SS, Zhu D. Genomic insights into the metabolic potential of a novel lignin-degrading and polyhydroxyalkanoates producing bacterium Pseudomonas sp. Hu109A. CHEMOSPHERE 2023; 310:136754. [PMID: 36228733 DOI: 10.1016/j.chemosphere.2022.136754] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/13/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
Lignin is the most abundant heterogeneous aromatic polymer present on planet Earth and is recalcitrant to degradation due to its complex structure, therefore, imposing a challenge to biorefinery procedures. Identifying new microbial strains with the potential to valorize lignin into useful compounds is indispensable to achieving green sustainable consumption. In this study, a novel Pseudomonas strain designated as Hu109A was isolated from the termite gut and the genome was sequenced and analyzed further. The genome contains a circular chromosome with the size of 5,131,917 bp having a GC content of 62.6% and 4698 genes. Genome annotation reveals that the strain possesses lignin-oxidizing enzymes such as DyP-type peroxidases, laccase, dioxygenase, and aromatic degradation gene clusters. The genome also contains O-methyltransferases which function in accelerating the lignin degradation by methylating the free hydroxyl phenolic compounds which in high concentration can inhibit the lignin peroxidase. Furthermore, the genome exhibits two gene clusters encoding the enzymes related to polyhydroxyalkanoates (PHA) synthesis. Pseudomonas strains are generally assumed to produce medium chain length PHAs (mcl-PHAs) only, however, strain Hu109A contains both Class II PHA synthase genes involved in mcl-PHAs and Class III PHA synthase gene involved in short-chain length PHAs (scl-PHAs). Gas Chromatography-Mass Spectrometry (GC-MS) analysis showed that using 1 g/L lignin as the sole carbon source, the maximum production of PHA observed was 103.68 mg/L, which increased to 186 mg/L with an increase in lignin concentration to 3 g/L. However, PHA production while using glucose as the sole carbon source was significantly lower than the lignin source, and maximum production was 125.6 mg/L with 3 g/L glucose. The strain Hu109A can tolerate a broad range of solvents including methanol, isopropanol, dimethylformamide, and ethanol, revealing its potential for industrial applications.
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Affiliation(s)
- Muhammad Zohaib Nawaz
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China; Department of Computer Science, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Huarong Shang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Alei Geng
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Sameh S Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China; Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Daochen Zhu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China.
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Optimization of Propagation Medium for Enhanced Polyhydroxyalkanoate Production by Pseudomonas oleovorans. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation8010016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Polyhydroxyalkanoates (PHAs) represent a promising alternative to commercially used petroleum-based plastics. Pseudomonas oleovorans is a natural producer of medium-chain-length PHA (mcl-PHA) under cultivation conditions with nitrogen limitation and carbon excess. Two-step cultivation appears to be an efficient but more expensive method of PHA production. Therefore, the aim of this work was to prepare a minimal synthetic medium for maximum biomass yield and to optimize selected independent variables by response surface methodology (RSM). The highest biomass yield (1.71 ± 0.04 g/L) was achieved in the optimized medium containing 8.4 g/L glucose, 5.7 g/L sodium ammonium phosphate and 35.4 mM phosphate buffer. Under these conditions, both carbon and nitrogen sources were completely consumed after 48 h of the cultivation and the biomass yield was 1.7-fold higher than in the conventional medium recommended by the literature. This approach demonstrates the possibility of using two-stage PHA cultivation to obtain the maximum amount of biomass and PHA.
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Zheng R, Li F, Li F, Gong A. Targeting tumor vascularization: promising strategies for vascular normalization. J Cancer Res Clin Oncol 2021; 147:2489-2505. [PMID: 34148156 DOI: 10.1007/s00432-021-03701-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/14/2021] [Indexed: 12/17/2022]
Abstract
Tumor recurrence after the clinical cure of tumor often results from the presence of an abnormal microenvironment, including an aberrant vasculature. The tumor microenvironment is rich in pro-angiogenic factors but lacks pro-maturation factors. Pro-angiogenic conditions in the tumor microenvironment, such as hypoxia, are double-edged swords, promoting both the repair of normal tissues and the development of an abnormal blood vessel network. The coexistence of perfusion and hypoxic zones and uneven blood vessel distribution in tumor tissues profoundly influence tumor deterioration, recurrence, and metastasis. Traditional anti-angiogenic therapies have shown limited efficacy, and promote drug resistance, and even metastasis. In contrast, vascular normalization therapy induces a more physiological-like state, leading to better outcomes and fewer side effects. Vascular normalization entails modifying the tumor vascular system to improve tumor oxygenation and substance transport, thereby contributing to improving the efficacy of radiotherapy, chemotherapy, and immunotherapy. This review mainly focuses on the process of tumor vascularization; potential therapeutic targets, including cells, metabolism, signaling pathways, and angiogenesis-related genes; and possible strategies to normalize blood vessels through regulating tumor vessel generation, the development of tumor vessels, and blood vessel fusion and pruning.
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Affiliation(s)
- Ruiqi Zheng
- Department of Cell Biology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212003, Jiangsu, China
| | - Feifan Li
- Department of Cell Biology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212003, Jiangsu, China
| | - Fengcen Li
- Department of Cell Biology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212003, Jiangsu, China
| | - Aihua Gong
- Department of Cell Biology, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212003, Jiangsu, China.
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