1
|
Gaur VK, Nguyen-Vo TP, Islam T, Bassey BF, Kim M, Ainala SK, Shin K, Park S. Efficient bioproduction of poly(3-hydroxypropionate) homopolymer using engineered Escherichia coli strains. BIORESOURCE TECHNOLOGY 2024; 397:130469. [PMID: 38382722 DOI: 10.1016/j.biortech.2024.130469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 02/23/2024]
Abstract
This study focuses on the development of a scalable method for producing poly(3-hydroxypropionate), a homopolymer with significant physico-mechanical properties, through the use of metabolically-engineered Escherichia coli K12 (MG1655) and externally supplied 3-hydroxypropionate. The polymer synthesis pathway was established and optimized through synthetic biology techniques, including the effects of overexpressing phasin and cell division proteins. The optimized strain achieved unprecedented production titers of 9.5 g/L in flask cultures and 80 g/L in fed-batch bioreactors within 45 h. The analysis of poly(3-hydroxypropionate) polymer properties revealed it possesses excellent elasticity (Young's modulus < 6 MPa) and tensile strength (∼80 MPa), positioning it within the category of elastomers or flexible plastics. These findings suggest a viable path for the sustainable, large-scale production of the poly(3-hydroxypropionate) biopolymer.
Collapse
Affiliation(s)
- Vivek Kumar Gaur
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Thuan Phu Nguyen-Vo
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; Presently: Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA
| | - Tayyab Islam
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Bassey Friday Bassey
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Miri Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Satish Kumar Ainala
- NOROO Bio R&D Center, NOROO Holdings Co., Ltd, Gyeonggi-do 16229, Republic of Korea
| | - Kyusoon Shin
- NOROO Bio R&D Center, NOROO Holdings Co., Ltd, Gyeonggi-do 16229, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
| |
Collapse
|
2
|
Aguilar-Carrillo Y, Soto-Urzúa L, Martínez-Martínez MDLÁ, Becerril-Ramírez M, Martínez-Morales LJ. Computational Analysis of the Tripartite Interaction of Phasins (PhaP4 and 5)-Sigma Factor (σ 24)-DNA of Azospirillum brasilense Sp7. Polymers (Basel) 2024; 16:611. [PMID: 38475295 DOI: 10.3390/polym16050611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 03/14/2024] Open
Abstract
Azospirillum brasilense Sp7 produces PHB, which is covered by granule-associated proteins (GAPs). Phasins are the main GAPs. Previous studies have shown phasins can regulate PHB synthesis. When A. brasilense grows under stress conditions, it uses sigma factors to transcribe genes for survival. One of these factors is the σ24 factor. This study determined the possible interaction between phasins and the σ24 factor or phasin-σ24 factor complex and DNA. Three-dimensional structures of phasins and σ24 factor structures were predicted using the I-TASSER and SWISS-Model servers, respectively. Subsequently, a molecular docking between phasins and the σ24 factor was performed using the ClusPro 2.0 server, followed by molecular docking between protein complexes and DNA using the HDOCK server. Evaluation of the types of ligand-receptor interactions was performed using the BIOVIA Discovery Visualizer for three-dimensional diagrams, as well as the LigPlot server to obtain bi-dimensional diagrams. The results showed the phasins (Pha4Abs7 or Pha5Abs7)-σ24 factor complex was bound near the -35 box of the promoter region of the phaC gene. However, in the individual interaction of PhaP5Abs7 and the σ24 factor, with DNA, both proteins were bound to the -35 box. This did not occur with PhaP4Abs7, which was bound to the -10 box. This change could affect the transcription level of the phaC gene and possibly affect PHB synthesis.
Collapse
Affiliation(s)
- Yovani Aguilar-Carrillo
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Lucía Soto-Urzúa
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - María De Los Ángeles Martínez-Martínez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Mirian Becerril-Ramírez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Luis Javier Martínez-Morales
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| |
Collapse
|
3
|
Quelas JI, Cabrera JJ, Díaz-Peña R, Sánchez-Schneider L, Jiménez-Leiva A, Tortosa G, Delgado MJ, Pettinari MJ, Lodeiro AR, del Val C, Mesa S. Pleiotropic Effects of PhaR Regulator in Bradyrhizobium diazoefficiens Microaerobic Metabolism. Int J Mol Sci 2024; 25:2157. [PMID: 38396833 PMCID: PMC10888616 DOI: 10.3390/ijms25042157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Bradyrhizobium diazoefficiens can live inside soybean root nodules and in free-living conditions. In both states, when oxygen levels decrease, cells adjust their protein pools by gene transcription modulation. PhaR is a transcription factor involved in polyhydroxyalkanoate (PHA) metabolism but also plays a role in the microaerobic network of this bacterium. To deeply uncover the function of PhaR, we applied a multipronged approach, including the expression profile of a phaR mutant at the transcriptional and protein levels under microaerobic conditions, and the identification of direct targets and of proteins associated with PHA granules. Our results confirmed a pleiotropic function of PhaR, affecting several phenotypes, in addition to PHA cycle control. These include growth deficiency, regulation of carbon and nitrogen allocation, and bacterial motility. Interestingly, PhaR may also modulate the microoxic-responsive regulatory network by activating the expression of fixK2 and repressing nifA, both encoding two transcription factors relevant for microaerobic regulation. At the molecular level, two PhaR-binding motifs were predicted and direct control mediated by PhaR determined by protein-interaction assays revealed seven new direct targets for PhaR. Finally, among the proteins associated with PHA granules, we found PhaR, phasins, and other proteins, confirming a dual function of PhaR in microoxia.
Collapse
Affiliation(s)
- Juan I. Quelas
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata 1900, Argentina; (J.I.Q.); (A.R.L.)
- YPF Tecnología S.A. (Y-TEC), Avenida. del Petróleo Argentino s/n (1923), Berisso 1923, Argentina
| | - Juan J. Cabrera
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - Rocío Díaz-Peña
- IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina; (R.D.-P.); (M.J.P.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina
| | - Lucía Sánchez-Schneider
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, 18016 Granada, Spain;
| | - Andrea Jiménez-Leiva
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - Germán Tortosa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - María J. Delgado
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| | - M. Julia Pettinari
- IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina; (R.D.-P.); (M.J.P.)
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes, C1428EHA, CABA, Buenos Aires 2160, Argentina
| | - Aníbal R. Lodeiro
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata 1900, Argentina; (J.I.Q.); (A.R.L.)
- Cátedra de Genética, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, La Plata 1900, Argentina
| | - Coral del Val
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, 18016 Granada, Spain;
| | - Socorro Mesa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.J.C.); (L.S.-S.); (A.J.-L.); (G.T.); (M.J.D.)
| |
Collapse
|
4
|
Blanco FG, Machatschek R, Keller M, Hernández-Arriaga AM, Godoy MS, Tarazona NA, Prieto MA. Nature-inspired material binding peptides with versatile polyester affinities and binding strengths. Int J Biol Macromol 2023; 253:126760. [PMID: 37683751 DOI: 10.1016/j.ijbiomac.2023.126760] [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: 06/17/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
Biodegradable polyesters, such as polyhydroxyalkanoates (PHAs), are having a tremendous impact on biomedicine. However, these polymers lack functional moieties to impart functions like targeted delivery of molecules. Inspired by native GAPs, such as phasins and their polymer-binding and surfactant properties, we generated small material binding peptides (MBPs) for polyester surface functionalization using a rational approach based on amphiphilicity. Here, two peptides of 48 amino acids derived from phasins PhaF and PhaI from Pseudomonas putida, MinP and the novel-designed MinI, were assessed for their binding towards two types of PHAs, PHB and PHOH. In vivo, fluorescence studies revealed selective binding towards PHOH, whilst in vitro binding experiments using the Langmuir-Blodgett technique coupled to ellipsometry showed KD in the range of nM for all polymers and MBPs. Marked morphological changes of the polymer surface upon peptide adsorption were shown by BAM and AFM for PHOH. Moreover, both MBPs were successfully used to immobilize cargo proteins on the polymer surfaces. Altogether, this work shows that by redesigning the amphiphilicity of phasins, a high affinity but lower specificity to polyesters can be achieved in vitro. Furthermore, the MBPs demonstrated binding to PET, showing potential to bind cargo molecules also to synthetic polyesters.
Collapse
Affiliation(s)
- Francisco G Blanco
- Polymer Biotechnology Group, Plant and Microbial Biotechnology Department, Margarita Salas Centre for Biological Research (CIB - CSIC), Madrid, Spain; Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Rainhard Machatschek
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513 Teltow, Germany
| | - Manuela Keller
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513 Teltow, Germany
| | - Ana M Hernández-Arriaga
- Polymer Biotechnology Group, Plant and Microbial Biotechnology Department, Margarita Salas Centre for Biological Research (CIB - CSIC), Madrid, Spain; Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Manuel S Godoy
- Polymer Biotechnology Group, Plant and Microbial Biotechnology Department, Margarita Salas Centre for Biological Research (CIB - CSIC), Madrid, Spain; Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Natalia A Tarazona
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, Kantstraße 55, 14513 Teltow, Germany.
| | - M Auxiliadora Prieto
- Polymer Biotechnology Group, Plant and Microbial Biotechnology Department, Margarita Salas Centre for Biological Research (CIB - CSIC), Madrid, Spain; Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
| |
Collapse
|
5
|
Blanco FG, Vázquez R, Hernández-Arriaga AM, García P, Prieto MA. Enzybiotic-mediated antimicrobial functionalization of polyhydroxyalkanoates. Front Bioeng Biotechnol 2023; 11:1220336. [PMID: 37449090 PMCID: PMC10336440 DOI: 10.3389/fbioe.2023.1220336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Polymeric nanoparticles (NPs) present some ideal properties as biomedical nanocarriers for targeted drug delivery such as enhanced translocation through body barriers. Biopolymers, such as polyhydroxyalkanoates (PHAs) are gaining attention as nanocarrier biomaterials due to their inherent biocompatibility, biodegradability, and ability to be vehiculized through hydrophobic media, such as the lung surfactant (LS). Upon colonization of the lung alveoli, below the LS layer, Streptococcus pneumoniae, causes community-acquired pneumonia, a severe respiratory condition. In this work, we convert PHA NPs into an antimicrobial material by the immobilization of an enzybiotic, an antimicrobial enzyme, via a minimal PHA affinity tag. We first produced the fusion protein M711, comprising the minimized PHA affinity tag, MinP, and the enzybiotic Cpl-711, which specifically targets S. pneumoniae. Then, a PHA nanoparticulate suspension with adequate physicochemical properties for pulmonary delivery was formulated, and NPs were decorated with M711. Finally, we assessed the antipneumococcal activity of the nanosystem against planktonic and biofilm forms of S. pneumoniae. The resulting system displayed sustained antimicrobial activity against both, free and sessile cells, confirming that tag-mediated immobilization of enzybiotics on PHAs is a promising platform for bioactive antimicrobial functionalization.
Collapse
Affiliation(s)
- Francisco G. Blanco
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Margarita Salas Center for Biological Research (CIB–CSIC), Madrid, Spain
- Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Roberto Vázquez
- Protein Engineering Against Antibiotic Resistance Group, Microbial and Plant Biotechnology Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Ana M. Hernández-Arriaga
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Margarita Salas Center for Biological Research (CIB–CSIC), Madrid, Spain
- Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Pedro García
- Protein Engineering Against Antibiotic Resistance Group, Microbial and Plant Biotechnology Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - M. Auxiliadora Prieto
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Margarita Salas Center for Biological Research (CIB–CSIC), Madrid, Spain
- Interdisciplinary Platform of Sustainable Plastics towards a Circular Economy, Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| |
Collapse
|
6
|
Kumar R, Li D, Luo L, Manu MK, Zhao J, Tyagi RD, Wong JWC. Genome-centric polyhydroxyalkanoate reconciliation reveals nutrient enriched growth dependent biosynthesis in Bacillus cereus IBA1. BIORESOURCE TECHNOLOGY 2023; 382:129210. [PMID: 37217149 DOI: 10.1016/j.biortech.2023.129210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023]
Abstract
Microbiological polyhydroxyalkanoates (PHAs) are rooted as the most promising bio-replacements of synthetic polymers. Inherent properties of these PHAs further expand their applicability in numerous industrial, environmental, and clinical sectors. To propel these, a new environmental, endotoxin free gram-positive bacterium i.e., Bacillus cereus IBA1 was identified to harbor advantageous PHA producer characteristics through high-throughput omics mining approaches. Unlike traditional fermentations, nutrient enriched strategy was used to enhance PHA granular concentrations by ∼2.3 folds to 2.78 ± 0.19 g/L. Additionally, this study is the first to confirm an underlying growth dependent PHA biogenesis through exploring PHA granule associated operons which harbour constitutively expressing PHA synthase (phaC) coupled with differentially expressing PHA synthase subunit (phaR) and regulatory protein (phaP, phaQ) amid different growth phases. Moreover, the feasibility of this promising microbial phenomenon could propel next-generation biopolymers, and increase industrial applicability of PHAs, thereby significantly contributing to the sustainable development.
Collapse
Affiliation(s)
- Rajat Kumar
- Institute of Bioresource and Agriculture and Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Dongyi Li
- Institute of Bioresource and Agriculture and Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Liwen Luo
- Institute of Bioresource and Agriculture and Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong
| | - M K Manu
- Institute of Bioresource and Agriculture and Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Jun Zhao
- Institute of Bioresource and Agriculture and Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Rajeshwar D Tyagi
- Institute of Bioresource and Agriculture and Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong
| | - Jonathan W C Wong
- Institute of Bioresource and Agriculture and Sino-Forest Applied Research Centre for Pearl River Delta Environment, Department of Biology, Hong Kong Baptist University, Hong Kong; Research Centre for Eco-environmental Engineering, Dongguan University of Technology, Dongguan 523830, PR China.
| |
Collapse
|
7
|
Complete genome sequence of Aquitalea pelogenes USM4 (JCM19919), a polyhydroxyalkanoate producer. Arch Microbiol 2023; 205:66. [PMID: 36645481 DOI: 10.1007/s00203-023-03406-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
Polyhydroxyalkanoate (PHA) is a type of biopolymer produced by most bacteria and archaea, resembling thermoplastic with biodegradability and biocompatibility features. Here, we report the complete genome of a PHA producer, Aquitalea sp. USM4, isolated from Perak, Malaysia. This bacterium possessed a 4.2 Mb circular chromosome and a 54,370 bp plasmid. A total of 4067 predicted protein-coding sequences, 87 tRNA genes, and 25 rRNA operons were identified using PGAP. Based on ANI and dDDH analysis, the Aquitalea sp. USM4 is highly similar to Aquitalea pelogenes. We also identified genes, including acetyl-CoA (phaA), acetoacetyl-CoA (phaB), PHA synthase (phaC), enoyl-CoA hydratase (phaJ), and phasin (phaP), which play an important role in PHA production in Aquitalea sp. USM4. The heterologous expression of phaC1 from Aquitalea sp. USM4 in Cupriavidus necator PHB-4 was able to incorporate six different types of PHA monomers, which are 3-hydroxybutyrate (3HB), 3-hydroxyvalerate (3HV), 4-hydroxybutyrate (4HB), 5-hydroxyvalerate (5HV), 3-hydroxyhexanoate (3HHx) and isocaproic acid (3H4MV) with suitable precursor substrates. This is the first complete genome sequence of the genus Aquitalea among the 22 genome sequences from 4 Aquitalea species listed in the GOLD database, which provides an insight into its genome evolution and molecular machinery responsible for PHA biosynthesis.
Collapse
|
8
|
Venkatakrishnan G, Parvathi VD. Decoding the mechanism of vascular morphogenesis to explore future prospects in targeted tumor therapy. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:178. [PMID: 36036322 DOI: 10.1007/s12032-022-01810-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/26/2022] [Indexed: 11/27/2022]
Abstract
The growth and formation of blood vessels is an undeniably fundamental biological process crucial to controlling overall development of an organism. This phenomenon consists of two separate processes, commencing with vasculogenesis, which refers to the process of blood vessel formation strictly in embryonic stages, via de novo endothelial cell synthesis. Angiogenesis continues the formation of the vascular network via sprouting and splitting. Tumor growth is dependent on the growth and supply of blood vessels around the tumor mass. Extracellular matrix (ECM) molecules can promote angiogenesis by establishing a vascular network and sequestering pro-angiogenic growth factors. Although the methods by which tumor-associated fibroblasts (which differ in phenotype from normal fibroblasts) influence angiogenesis are unknown, they are thought to be a major source of growth factors and cytokines that attract endothelial cells. Chemokines and growth factors (sourced from macrophages and neutrophils) are also regulators of angiogenesis. When considered as a whole, the tumor microenvironment is a heterogenous and dynamic mass of tissue, composed of a plethora of cell types and an ECM that can fundamentally control the pathological angiogenic switch. Angiogenesis is involved in numerous diseases, and understanding the various mechanisms surrounding this phenomenon is key to finding cures.
Collapse
Affiliation(s)
- Gayathri Venkatakrishnan
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, 600116, India
| | - Venkatachalam Deepa Parvathi
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, 600116, India.
| |
Collapse
|
9
|
Shahrear S, Afroj Zinnia M, Sany MRU, Islam ABMMK. Functional Analysis of Hypothetical Proteins of Vibrio parahaemolyticus Reveals the Presence of Virulence Factors and Growth-Related Enzymes With Therapeutic Potential. Bioinform Biol Insights 2022; 16:11779322221136002. [PMID: 36386863 PMCID: PMC9661560 DOI: 10.1177/11779322221136002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/30/2022] [Indexed: 11/11/2022] Open
Abstract
Vibrio parahaemolyticus, an aquatic pathogen, is a major concern in the shrimp aquaculture industry. Several strains of this pathogen are responsible for causing acute hepatopancreatic necrosis disease as well as other serious illness, both of which result in severe economic losses. The genome sequence of two pathogenic strains of V. parahaemolyticus, MSR16 and MSR17, isolated from Bangladesh, have been reported to gain a better understanding of their diversity and virulence. However, the prevalence of hypothetical proteins (HPs) makes it challenging to obtain a comprehensive understanding of the pathogenesis of V. parahaemolyticus. The aim of the present study is to provide a functional annotation of the HPs to elucidate their role in pathogenesis employing several in silico tools. The exploration of protein domains and families, similarity searches against proteins with known function, gene ontology enrichment, along with protein-protein interaction analysis of the HPs led to the functional assignment with a high level of confidence for 656 proteins out of a pool of 2631 proteins. The in silico approach used in this study was important for accurately assigning function to HPs and inferring interactions with proteins with previously described functions. The HPs with function predicted were categorized into various groups such as enzymes involved in small-compound biosynthesis pathway, iron binding proteins, antibiotics resistance proteins, and other proteins. Several proteins with potential druggability were identified among them. In addition, the HPs were investigated in search of virulent factors, which led to the identification of proteins that have the potential to be exploited as vaccine candidate. The findings of the study will be effective in gaining a better understanding of the molecular mechanisms of bacterial pathogenesis. They may also provide an insight into the process of evaluating promising targets for the development of drugs and vaccines against V. parahaemolyticus.
Collapse
Affiliation(s)
- Sazzad Shahrear
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | | | - Md. Rabi Us Sany
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | | |
Collapse
|
10
|
Müller-Santos M, Koskimäki JJ, Alves LPS, de Souza EM, Jendrossek D, Pirttilä AM. The protective role of PHB and its degradation products against stress situations in bacteria. FEMS Microbiol Rev 2021; 45:fuaa058. [PMID: 33118006 DOI: 10.1093/femsre/fuaa058] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022] Open
Abstract
Many bacteria produce storage biopolymers that are mobilized under conditions of metabolic adaptation, for example, low nutrient availability and cellular stress. Polyhydroxyalkanoates are often found as carbon storage in Bacteria or Archaea, and of these polyhydroxybutyrate (PHB) is the most frequently occurring PHA type. Bacteria usually produce PHB upon availability of a carbon source and limitation of another essential nutrient. Therefore, it is widely believed that the function of PHB is to serve as a mobilizable carbon repository when bacteria face carbon limitation, supporting their survival. However, recent findings indicate that bacteria switch from PHB synthesis to mobilization under stress conditions such as thermal and oxidative shock. The mobilization products, 3-hydroxybutyrate and its oligomers, show a protective effect against protein aggregation and cellular damage caused by reactive oxygen species and heat shock. Thus, bacteria should have an environmental monitoring mechanism directly connected to the regulation of the PHB metabolism. Here, we review the current knowledge on PHB physiology together with a summary of recent findings on novel functions of PHB in stress resistance. Potential applications of these new functions are also presented.
Collapse
Affiliation(s)
- Marcelo Müller-Santos
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Janne J Koskimäki
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, P.O. Box 3000, FI-90014 Oulu, Finland
| | - Luis Paulo Silveira Alves
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná - UFPR, Setor de Ciências Biológicas, Centro Politécnico, Jardim da Américas, CEP: 81531-990, Caixa Postal: 190-46, Curitiba, Paraná, Brazil
| | - Dieter Jendrossek
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Anna Maria Pirttilä
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, P.O. Box 3000, FI-90014 Oulu, Finland
| |
Collapse
|
11
|
Bio-specific immobilization of enzymes on electrospun PHB nanofibers. Enzyme Microb Technol 2021; 145:109749. [PMID: 33750539 DOI: 10.1016/j.enzmictec.2021.109749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/16/2021] [Accepted: 01/18/2021] [Indexed: 11/21/2022]
Abstract
Enzyme immobilization provides substantial advantages in terms of improving the efficiency of enzymatic process as well as enhancing the reusability of enzymes. Phasins (PhaPs) are naturally occurring polyhydroxyalkanoate (PHA)-binding proteins, and thus can potentially be used as a fusion partner for oriented immobilization of enzymes onto PHA supports. However, presently available granular PHA supports have low surface-area-to-volume ratio and limited configurational flexibility of enzymatic reactions. In this study, we explored the use of electrospun polyhydroxybutyrate (PHB) nanofibers as an alternative support for high density immobilization of a PhaP-fused lipase. As envisioned, the electrospun PHB nanofibers could anchor 120-fold more enzyme than PHB granules of the same weight. Furthermore, the enzymes immobilized onto the PHB nanofibers exhibited markedly higher stability and activity compared to when immobilized on conventional immobilization supports. Our approach combines the advantageous features of nanofibrous material and specificity of biomolecular interaction for the efficient use of enzymes, which can be widely adopted in the development of various enzymatic processes.
Collapse
|
12
|
Mato A, Blanco FG, Maestro B, Sanz JM, Pérez-Gil J, Prieto MA. Dissecting the Polyhydroxyalkanoate-Binding Domain of the PhaF Phasin: Rational Design of a Minimized Affinity Tag. Appl Environ Microbiol 2020; 86:e00570-20. [PMID: 32303541 PMCID: PMC7267194 DOI: 10.1128/aem.00570-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/10/2020] [Indexed: 12/13/2022] Open
Abstract
Phasin PhaF from Pseudomonas putida consists of a modular protein whose N-terminal domain (BioF) has been demonstrated to be responsible for binding to the polyhydroxyalkanoate (PHA) granule. BioF has been exploited for biotechnological purposes as an affinity tag in the functionalization of PHA beads with fusion proteins both in vivo and in vitro The structural model of this domain suggests an amphipathic α-helical conformation with the hydrophobic residues facing the PHA granule. In this work, we analyzed the mean hydrophobicity and the hydrophobic moment of the native BioF tag to rationally design shorter versions that maintain affinity for the granule. Hybrid proteins containing the green fluorescent protein (GFP) fused to the BioF derivatives were studied for in vivo localization on PHA, stability on the surface of the PHA granule against pH, temperature, and ionic strength, and their possible influence on PHA synthesis. Based on the results obtained, a minimized BioF tag for PHA functionalization has been proposed (MinP) that retains similar binding properties but possesses an attractive biotechnological potential derived from its reduced size. The MinP tag was further validated by analyzing the functionality and stability of the fusion proteins MinP-β-galactosidase and MinP-CueO from Escherichia coliIMPORTANCE Polyhydroxyalkanoates (PHAs) are biocompatible, nontoxic, and biodegradable biopolymers with exceptional applications in the industrial and medical fields. The complex structure of the PHA granule can be exploited as a toolbox to display molecules of interest on their surface. Phasins, the most abundant group of proteins on the granule, have been employed as anchoring tags to obtain functionalized PHA beads for high-affinity bioseparation, enzyme immobilization, diagnostics, or cell targeting. Here, a shorter module based on the previously designed BioF tag has been demonstrated to maintain the affinity for the PHA granule, with higher stability and similar functionalization efficiency. The use of a 67% shorter peptide, which maintains the binding properties of the entire protein, constitutes an advantage for the immobilization of recombinant proteins on the PHA surface both in vitro and in vivo.
Collapse
Affiliation(s)
- Aranzazu Mato
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Francisco G Blanco
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Beatriz Maestro
- Host-Parasite Interplay in Pneumococcal Infection Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
| | - Jesús M Sanz
- Host-Parasite Interplay in Pneumococcal Infection Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Jesús Pérez-Gil
- Biochemical and Molecular Biology Department, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - M Auxiliadora Prieto
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| |
Collapse
|
13
|
Novel unexpected functions of PHA granules. Appl Microbiol Biotechnol 2020; 104:4795-4810. [PMID: 32303817 DOI: 10.1007/s00253-020-10568-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
Polyhydroxyalkanoates (PHA), polyesters accumulated by numerous prokaryotes in the form of intracellular granules, have been for decades considered being predominantly storage molecules. However, numerous recent discoveries revealed and emphasized their complex biological role for microbial cells. Most of all, it was repeatedly reported and confirmed that the presence of PHA granules in prokaryotic cells enhances stress resistance and robustness of microbes against various environmental stress factors such as high or low temperature, freezing, oxidative, and osmotic pressure. It seems that protective mechanisms of PHA granules are associated with their extraordinary architecture and biophysical properties as well as with the complex and deeply interconnected nature of PHA metabolism. Therefore, this review aims at describing novel and unexpected properties of PHA granules with respect to their contribution to stress tolerance of various prokaryotes including common mesophilic heterotrophic bacteria, but also extremophiles or photo-autotrophic cyanobacteria. KEY POINTS: • PHA granules present in bacterial cells reveal unique properties and functions. • PHA enhances stress robustness of bacterial cells.
Collapse
|
14
|
Wong JX, Ogura K, Chen S, Rehm BHA. Bioengineered Polyhydroxyalkanoates as Immobilized Enzyme Scaffolds for Industrial Applications. Front Bioeng Biotechnol 2020; 8:156. [PMID: 32195237 PMCID: PMC7064635 DOI: 10.3389/fbioe.2020.00156] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/14/2020] [Indexed: 12/11/2022] Open
Abstract
Enzymes function as biocatalysts and are extensively exploited in industrial applications. Immobilization of enzymes using support materials has been shown to improve enzyme properties, including stability and functionality in extreme conditions and recyclability in biocatalytic processing. This review focuses on the recent advances utilizing the design space of in vivo self-assembled polyhydroxyalkanoate (PHA) particles as biocatalyst immobilization scaffolds. Self-assembly of biologically active enzyme-coated PHA particles is a one-step in vivo production process, which avoids the costly and laborious in vitro chemical cross-linking of purified enzymes to separately produced support materials. The homogeneous orientation of enzymes densely coating PHA particles enhances the accessibility of catalytic sites, improving enzyme function. The PHA particle technology has been developed into a remarkable scaffolding platform for the design of cost-effective designer biocatalysts amenable toward robust industrial bioprocessing. In this review, the PHA particle technology will be compared to other biological supramolecular assembly-based technologies suitable for in vivo enzyme immobilization. Recent progress in the fabrication of biological particulate scaffolds using enzymes of industrial interest will be summarized. Additionally, we outline innovative approaches to overcome limitations of in vivo assembled PHA particles to enable fine-tuned immobilization of multiple enzymes to enhance performance in multi-step cascade reactions, such as those used in continuous flow bioprocessing.
Collapse
Affiliation(s)
- Jin Xiang Wong
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- MacDiarmid Institute of Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington, New Zealand
| | - Kampachiro Ogura
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Shuxiong Chen
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - Bernd H. A. Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
- Menzies Health Institute Queensland (MHIQ), Griffith University, Gold Coast Campus, Southport, QLD, Australia
| |
Collapse
|
15
|
Tao W, Lin J, Wang W, Huang H, Li S. Designer bioemulsifiers based on combinations of different polysaccharides with the novel emulsifying esterase AXE from Bacillus subtilis CICC 20034. Microb Cell Fact 2019; 18:173. [PMID: 31601224 PMCID: PMC6786282 DOI: 10.1186/s12934-019-1221-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 09/27/2019] [Indexed: 12/19/2022] Open
Abstract
Background Bioemulsifiers are surface-active compounds, which exhibit advantages including low toxicity, higher biodegradability and biocompatibility over synthetic chemical surfactants. Despite their potential benefits, some obstacles impede the practical applications of bioemulsifiers, including low yields and high purification costs. Here, we aimed to exploit a novel protein bioemulsifier with efficient emulsifying activity and low-production cost, as well as proposed a design-bioemulsifier system that meets different requirements of industrial emulsification in the most economical way. Results The esterase AXE was first reported for its efficient emulsifying activity and had been studied for possible application as a protein bioemulsifier. AXE showed an excellent emulsification effect with different hydrophobic substrates, especially short-chain aliphatic and benzene derivatives, as well as excellent stability under extreme conditions such as high temperature (85 °C) and acidic conditions. AXE also exhibited good stability over a range of NaCl, MgSO4, and CaCl2 concentrations from 0 to 1000 mM, and the emulsifying activity even showed a slight increase at salt concentrations over 500 mM. A design-bioemulsifier system was proposed that uses AXE in combination with a variety of polysaccharides to form efficient bioemulsifier, which enhanced the emulsifying activity and further lowered the concentration of AXE needed in the complex. Conclusions AXE showed a great application potential as a novel bioemulsifier with excellent emulsifying ability. The AXE-based-designer bioemulsifier could be obtained in the most economical way and open broad new fields for low-cost, environmentally friendly bioemulsifiers.![]()
Collapse
Affiliation(s)
- Weiyi Tao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Junzhang Lin
- Oil Production Research Institute, Shengli Oil Field Ltd. Co. SinoPEC, Dongying, China
| | - Weidong Wang
- Oil Production Research Institute, Shengli Oil Field Ltd. Co. SinoPEC, Dongying, China
| | - He Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Shuang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China.
| |
Collapse
|
16
|
Moreno S, Castellanos M, Bedoya-Pérez LP, Canales-Herrerías P, Espín G, Muriel-Millán LF. Outer membrane protein I is associated with poly-β-hydroxybutyrate granules and is necessary for optimal polymer accumulation in Azotobacter vinelandii on solid medium. Microbiology (Reading) 2019; 165:1107-1116. [DOI: 10.1099/mic.0.000837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Soledad Moreno
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Mildred Castellanos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
- Present address: Department of Biochemistry and Molecular Biology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Leidy Patricia Bedoya-Pérez
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
- Present address: Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Pablo Canales-Herrerías
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
- Present address: Institut Pasteur, Department of Immunology, Unit of Antibodies in Therapy and Pathology, Paris, France
| | - Guadalupe Espín
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| | - Luis Felipe Muriel-Millán
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, México
| |
Collapse
|
17
|
Martínez-Martínez MDLA, González-Pedrajo B, Dreyfus G, Soto-Urzúa L, Martínez-Morales LJ. Phasin PhaP1 is involved in polyhydroxybutyrate granules morphology and in controlling early biopolymer accumulation in Azospirillum brasilense Sp7. AMB Express 2019; 9:155. [PMID: 31555910 PMCID: PMC6761214 DOI: 10.1186/s13568-019-0876-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/09/2019] [Indexed: 11/10/2022] Open
Abstract
Phasins are amphiphilic proteins involved in the regulation of the number and size of polyhydroxybutyrate (PHB) granules. The plant growth promoting bacterium Azospirillum brasilense Sp7 accumulates high quantities of bioplastic PHB as carbon and energy source. By analyzing the genome, we identified six genes that code for proteins with a Phasin_2 domain. To understand the role of A. brasilense Sp7 PhaP1 (PhaP1Abs) on PHB synthesis, the phaP1 gene (AMK58_RS17065) was deleted. The morphology of the PHB granules was analyzed by transmission electron microscopy (TEM) and the PHB produced was quantified under three different C:N ratios in cultures subjected to null or low-oxygen transfer. The results showed that PhaP1Abs is involved in PHB granules morphology and in controlling early biopolymer accumulation. Using RT-PCR it was found that phasin genes, except phaP4, are transcribed in accordance with the C:N ratio used for the growth of A. brasilense. phaP1, phaP2 and phaP3 genes were able to respond to the growth conditions tested. This study reports the first analysis of a phasin protein in A. brasilense Sp7.
Collapse
|
18
|
Fan F, Wu X, Zhao J, Ran G, Shang S, Li M, Lu X. A Specific Drug Delivery System for Targeted Accumulation and Tissue Penetration in Prostate Tumors Based on Microbially Synthesized PHBHHx Biopolyester and iRGD Peptide Fused PhaP. ACS APPLIED BIO MATERIALS 2018; 1:2041-2053. [DOI: 10.1021/acsabm.8b00524] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Fan Fan
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, P. R. China
| | - Xingjuan Wu
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, P. R. China
| | - Jiping Zhao
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, P. R. China
| | - Ganqiao Ran
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, P. R. China
| | - Sen Shang
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, P. R. China
| | - Mingchuan Li
- Molecular Biotechnology Center, Universita di Torino, 10126 Torino, Italy
| | - Xiaoyun Lu
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, P. R. China
| |
Collapse
|
19
|
Tarazona NA, Maestro B, Revelles O, Sanz JM, Prieto MA. Role of leucine zipper-like motifs in the oligomerization of Pseudomonas putida phasins. Biochim Biophys Acta Gen Subj 2018; 1863:362-370. [PMID: 30419286 DOI: 10.1016/j.bbagen.2018.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND Phasins are low molecular mass proteins that accumulate strongly in bacterial cells in response to the intracellular storage of polyhydroxyalkanoates (PHA). Although lacking catalytic activity, phasins are the major components of the surface of the PHA granules and could be potentially involved in the formation of a network-like protein layer surrounding the polyester inclusions. Structural models revealed phasins to possess coiled-coil regions that might be important in the establishment of protein-protein interactions. However, there is not experimental evidence of a coiled-coil mediated oligomerization in these proteins. METHODS Structure prediction analyses were used to characterize the coiled-coil motifs of phasins PhaF and PhaI -produced by the model bacterium Pseudomonas putida KT2440-. Their oligomerization was evaluated by biolayer interferometry and the in vivo two-hybrid (BACTH) system. The interaction ability of a series of coiled-coil mutated derivatives was also measured. RESULTS The formation of PhaF and PhaI complexes was detected. A predicted short leucine zipper-like coiled-coil (ZIP), containing "ideal" residues located within the hydrophobic core, was shown responsible for the oligomers stability. The substitution of key residues (leucines or valines) in PhaI ZIP (ZIPI) for alanine reduced by four fold the oligomerization efficiency. CONCLUSIONS These results indicate that coiled-coil motifs are essential for phasin interactions. Correct oligomerization requires the formation of a stable hydrophobic interface between both phasins. GENERAL SIGNIFICANCE Our findings elucidate the oligomerization motif of PhaF and PhaI. This motif is present in most phasins from PHA-accumulating bacteria and offers a potentially important target for modulating the PHA granules stability.
Collapse
Affiliation(s)
- Natalia A Tarazona
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, CSIC, Madrid 28040, Spain
| | - Beatriz Maestro
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche 03202, Spain
| | - Olga Revelles
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, CSIC, Madrid 28040, Spain
| | - Jesús M Sanz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, CSIC, Madrid 28040, Spain; Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche 03202, Spain
| | - M Auxiliadora Prieto
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, CSIC, Madrid 28040, Spain.
| |
Collapse
|
20
|
Sagong HY, Son HF, Choi SY, Lee SY, Kim KJ. Structural Insights into Polyhydroxyalkanoates Biosynthesis. Trends Biochem Sci 2018; 43:790-805. [PMID: 30139647 DOI: 10.1016/j.tibs.2018.08.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/27/2018] [Accepted: 08/04/2018] [Indexed: 12/25/2022]
Abstract
Polyhydroxyalkanoates (PHAs) are diverse biopolyesters produced by numerous microorganisms and have attracted much attention as a substitute for petroleum-based polymers. Despite several decades of study, the detailed molecular mechanisms of PHA biosynthesis have remained unknown due to the lack of structural information on the key PHA biosynthetic enzyme PHA synthase. The recently determined crystal structure of PHA synthase, together with the structures of acetyl-coenzyme A (CoA) acetyltransferase and reductase, have changed this situation. Structural and biochemical studies provided important clues for the molecular mechanisms of each enzyme as well as the overall mechanism of PHA biosynthesis from acetyl-CoA. This new information and knowledge is expected to facilitate production of designed novel PHAs and also enhanced production of PHAs.
Collapse
Affiliation(s)
- Hye-Young Sagong
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyeoncheol Francis Son
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.
| |
Collapse
|
21
|
Reprogramming Halomonas for industrial production of chemicals. J Ind Microbiol Biotechnol 2018; 45:545-554. [PMID: 29948194 DOI: 10.1007/s10295-018-2055-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/31/2018] [Indexed: 12/26/2022]
Abstract
Halomonas spp. are able to grow under a high salt concentration at alkali pH, they are able to resist contamination by other microbes. Development of Halomonas spp. as platform production strains for the next-generation industrial biotechnology (NGIB) is intensively studied. Among Halomonas spp., Halomonas bluephagenesis is the best studied one with available engineering tools and methods to reprogram it for production of various polyhydroxyalkanoates, proteins, and chemicals. Due to its contamination resistance, H. bluephagenesis can be grown under open and continuous processes not just in the labs but also in at least 1000 L fermentor scale. It is expected that NGIB based on Halomonas spp. be able to engineer for production of increasing number of products in a competitive manner.
Collapse
|
22
|
Xiao-Ran J, Jin Y, Xiangbin C, Guo-Qiang C. Halomonas and Pathway Engineering for Bioplastics Production. Methods Enzymol 2018; 608:309-328. [PMID: 30173767 DOI: 10.1016/bs.mie.2018.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Traditional microbial chassis, including Escherichia coli, Bacillus subtilis, Ralstonia eutropha, and Pseudomonas putida, are grown under neutral pH and mild osmotic pressure for production of chemicals and materials. They tend to be contaminated easily by many microorganisms. To address this issue, next-generation industrial biotechnology employing halophilic Halomonas spp. has been developed for production of bioplastics polyhydroxyalkanoates (PHAs) and other chemicals. Halomonas spp. that can be grown contamination free under open and unsterile condition at alkali pH and high NaCl have been engineered to produce several PHA polymers in elongated or enlarged cells. New pathways can also be constructed both in plasmids and on chromosomes for Halomonas spp. Synthetic biology approaches and parts have been developed for Halomonas spp., allowing better control of their growth and product formation as well as morphology adjustment. Halomonas spp. and their synthetic biology will play an increasingly important role for industrial production of large volume chemicals.
Collapse
Affiliation(s)
- Jiang Xiao-Ran
- MOE Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yin Jin
- MOE Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Chen Xiangbin
- MOE Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Chen Guo-Qiang
- MOE Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China; Manchester Institute of Biotechnology, Centre for Synthetic Biology, The University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
23
|
Fan F, Wang L, Ouyang Z, Wen Y, Lu X. Development and optimization of a tumor targeting system based on microbial synthesized PHA biopolymers and PhaP mediated functional modification. Appl Microbiol Biotechnol 2018; 102:3229-3241. [PMID: 29497797 DOI: 10.1007/s00253-018-8790-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 01/14/2018] [Accepted: 01/15/2018] [Indexed: 01/08/2023]
Abstract
Polyhydroxyalkanoate (PHA) is a class of microbial synthesized biodegradable and biocompatible aliphatic polymer which has been developed into nanoparticles (NPs) for sustained release of hydrophobic compounds. Taking advantage of the natural PHA binding protein PhaP which could be steadily adsorbed onto PHA NPs through hydrophobic interaction, a tumor targeting system was developed in this study by presenting an epidermal growth factor receptor (EGFR)-targeting peptide (ETP) on the surface of PHA NPs, via PhaP mediated adsorption. To reveal the effects of residual emulsifiers on PhaP mediated ETP modification and optimize the tumor targeting capacity of the system, a novel emulsifier-free PHA NPs (EF-NPs) was fabricated together with other two kinds of conventional emulsifier-required PHA NPs (PVA-NPs and P68-NPs, which were prepared with poly(vinyl alcohol) (PVA) and Pluronic F68 as emulsifiers, respectively). By analyzing the surface hydrophobicity, the amount of adsorbed fusion protein, and the cellular uptake of all kinds of PHA NPs, our results demonstrated that EF-NPs with stronger surface hydrophobicity were the most proper formulation for further PhaP mediated ETP functionalization. The residual PVA and Pluronic F68 affected the modification efficiency and secondary structure of ETP-PhaP fusion protein, and finally obstructed the targeting effect of ETP-PhaP modified PVA-NPs and P68-NPs to EGFR over-expressed tumor cells. The animal experiment further confirmed the effectiveness and feasibility of in vivo application of ETP-PhaP functionalized EF-NPs, indicating that it could be served as a promising tumor targeting system with satisfactory EGFR targeting ability. This PhaP mediated bio-modification process also opens a wide way for developing various PHA-based targeting systems by presenting different tumor or other tissue-specific targeting peptides.
Collapse
Affiliation(s)
- Fan Fan
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Leilei Wang
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Zhenlin Ouyang
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Yurong Wen
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China
| | - Xiaoyun Lu
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, People's Republic of China.
| |
Collapse
|
24
|
The fight for invincibility: Environmental stress response mechanisms and Aeromonas hydrophila. Microb Pathog 2018; 116:135-145. [PMID: 29355702 DOI: 10.1016/j.micpath.2018.01.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 01/15/2018] [Accepted: 01/15/2018] [Indexed: 12/11/2022]
Abstract
Aeromonas hydrophila is a freshwater-dwelling zoonotic bacterium that has economic importance in aquaculture. In the past decade, Aeromonas hydrophila has become increasingly important because of its emergence as a food-borne zoonotic pathogen that is resistant to different treatment regimes. Being an aquatic bacterium, Aeromonas hydrophila is frequently subjected to several stressful environmental conditions, including changes in temperature, acidic pH and starvation that challenge its survival. To cope with these stressful conditions, like every cell, A. hydrophila possesses stress response mechanisms, such as alternative sigma factors, two-component systems, heat shock proteins, cold shock proteins, and acid tolerance response systems that eventually lead the fittest to survive. Moreover, the establishment of genetic variations among the strains related to environmental stress is also of great concern. This review presents the understandings based on inter-strain variations and stress response behavior of A. hydrophila that are important to control the increasing outbreaks of this bacterium in both human populations and aquaculture.
Collapse
|
25
|
Engineering cell wall synthesis mechanism for enhanced PHB accumulation in E. coli. Metab Eng 2018; 45:32-42. [DOI: 10.1016/j.ymben.2017.11.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/18/2017] [Accepted: 11/18/2017] [Indexed: 11/23/2022]
|
26
|
Maestro B, Sanz JM. Polyhydroxyalkanoate-associated phasins as phylogenetically heterogeneous, multipurpose proteins. Microb Biotechnol 2017; 10:1323-1337. [PMID: 28425176 PMCID: PMC5658603 DOI: 10.1111/1751-7915.12718] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/19/2017] [Accepted: 03/22/2017] [Indexed: 01/01/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs) are natural polyesters of increasing biotechnological importance that are synthesized by many prokaryotic organisms as carbon and energy storage compounds in limiting growth conditions. PHAs accumulate intracellularly in form of inclusion bodies that are covered with a proteinaceous surface layer (granule-associated proteins or GAPs) conforming a network-like surface of structural, metabolic and regulatory polypeptides, and configuring the PHA granules as complex and well-organized subcellular structures that have been designated as 'carbonosomes'. GAPs include several enzymes related to PHA metabolism (synthases, depolymerases and hydroxylases) together with the so-called phasins, an heterogeneous group of small-size proteins that cover most of the PHA granule and that are devoid of catalytic functions but nevertheless play an essential role in granule structure and PHA metabolism. Structurally, phasins are amphiphilic proteins that shield the hydrophobic polymer from the cytoplasm. Here, we summarize the characteristics of the different phasins identified so far from PHA producer organisms and highlight the diverse opportunities that they offer in the Biotechnology field.
Collapse
Affiliation(s)
- Beatriz Maestro
- Instituto de Biología Molecular y CelularUniversidad Miguel HernándezAv. Universidad s/nElche03202Spain
| | - Jesús M. Sanz
- Instituto de Biología Molecular y CelularUniversidad Miguel HernándezAv. Universidad s/nElche03202Spain
| |
Collapse
|
27
|
Zhao H, Yao Z, Chen X, Wang X, Chen GQ. Modelling of microbial polyhydroxyalkanoate surface binding protein PhaP for rational mutagenesis. Microb Biotechnol 2017; 10:1400-1411. [PMID: 28840964 PMCID: PMC5658623 DOI: 10.1111/1751-7915.12820] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/07/2017] [Accepted: 07/13/2017] [Indexed: 02/05/2023] Open
Abstract
Phasins are unusual amphiphilic proteins that bind to microbial polyhydroxyalkanoate (PHA) granules in nature and show great potential for various applications in biotechnology and medicine. Despite their remarkable diversity, only the crystal structure of PhaPAh from Aeromonas hydrophila has been solved to date. Based on the structure of PhaPAh, homology models of PhaPAz from Azotobacter sp. FA‐8 and PhaPTD from Halomonas bluephagenesis TD were successfully established, allowing rational mutagenesis to be conducted to enhance the stability and surfactant properties of these proteins. PhaPAz mutants, including PhaPAzQ38L and PhaPAzQ78L, as well as PhaPTD mutants, including PhaPTDQ38M and PhaPTDQ72M, showed better emulsification properties and improved thermostability (6‐10°C higher melting temperatures) compared with their wild‐type homologues under the same conditions. Importantly, the established PhaP homology‐modelling approach, based on the high‐resolution structure of PhaPAh, can be generalized to facilitate the study of other PhaP members.
Collapse
Affiliation(s)
- Hongyu Zhao
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Zhenyu Yao
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiangbin Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xinquan Wang
- MOE Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.,Center for Nano and Micro-Mechanics, Tsinghua University, Beijing, 100084, China.,MOE Key Lab for Industrial Biocatalysis, Tsinghua University, Beijing, 100084, China
| |
Collapse
|