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Zhang Y, Zhang T, Li M, Miao M. Rational design to improve the catalytic efficiency and stability of arginine deiminase. Int J Biol Macromol 2024; 269:132083. [PMID: 38705327 DOI: 10.1016/j.ijbiomac.2024.132083] [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: 12/20/2023] [Revised: 04/10/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Arginine deiminase (ADI) has garnered significant interest because of its ability to objectively eradicate cancer cells and produce L-citrulline. To meet the production demands, this study focused on enhancing the enzyme activity and thermal stability of ADI. In this study, 24 ADI mutants were obtained through computer aid site-specific mutation in the ADI of Enterobacter faecalis. Notably, the specific enzyme activities of F44W, N163P, E220I, E220L, N318E, A336G, T340I, and N382F increased, reaching 1.33-2.53 times that of the original enzyme. This study confirmed that site-specific mutations are critical for optimizing enzyme function. Additionally, the F44W, N163P, E220I, T340I, and A336G mutants demonstrated good thermal stability. The optimal pH for mutant F44W increased to 8, whereas mutants E220I, I244V, A336G, T340I, and N328F maintained an optimal pH of 7.5. Conversely, the M109L, N163P, E220L, I244L, and N318E mutants shad an optimal pH of 7. This study revealed that mutant enzymes with increased activity were more likely to contain mutation sites situated near the four loops associated with catalytic residues, whereas mutations at the dimer junction sites had a higher tendency to enhance enzyme stability. These findings contribute to the development of ADI industrial applications and its modifications.
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Affiliation(s)
- Yijing Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Mengli Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ming Miao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Science and Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
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2
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Molina-Henares MA, Ramos-González MI, Rinaldo S, Espinosa-Urgel M. Gene expression reprogramming of Pseudomonas alloputida in response to arginine through the transcriptional regulator ArgR. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001449. [PMID: 38511653 PMCID: PMC10963909 DOI: 10.1099/mic.0.001449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Different bacteria change their life styles in response to specific amino acids. In Pseudomonas putida (now alloputida) KT2440, arginine acts both as an environmental and a metabolic indicator that modulates the turnover of the intracellular second messenger c-di-GMP, and expression of biofilm-related genes. The transcriptional regulator ArgR, belonging to the AraC/XylS family, is key for the physiological reprogramming in response to arginine, as it controls transport and metabolism of the amino acid. To further expand our knowledge on the roles of ArgR, a global transcriptomic analysis of KT2440 and a null argR mutant growing in the presence of arginine was carried out. Results indicate that this transcriptional regulator influences a variety of cellular functions beyond arginine metabolism and transport, thus widening its regulatory role. ArgR acts as positive or negative modulator of the expression of several metabolic routes and transport systems, respiratory chain and stress response elements, as well as biofilm-related functions. The partial overlap between the ArgR regulon and those corresponding to the global regulators RoxR and ANR is also discussed.
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Affiliation(s)
- María Antonia Molina-Henares
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC. Profesor Albareda, 1. Granada 18008, Spain
| | - María Isabel Ramos-González
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC. Profesor Albareda, 1. Granada 18008, Spain
| | - Serena Rinaldo
- Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti - Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy
| | - Manuel Espinosa-Urgel
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC. Profesor Albareda, 1. Granada 18008, Spain
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3
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Wang Y, Gallagher LA, Andrade PA, Liu A, Humphreys IR, Turkarslan S, Cutler KJ, Arrieta-Ortiz ML, Li Y, Radey MC, McLean JS, Cong Q, Baker D, Baliga NS, Peterson SB, Mougous JD. Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle. Cell 2023; 186:4803-4817.e13. [PMID: 37683634 PMCID: PMC10633639 DOI: 10.1016/j.cell.2023.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023]
Abstract
Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute a disproportionately large fraction of microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow as epibionts on host Actinobacteria. Due to a lack of suitable tools, the genetic basis of this lifestyle and other unique features of Patescibacteira remain unexplored. Here, we show that Saccharibacteria exhibit natural competence, and we exploit this property for their genetic manipulation. Imaging of fluorescent protein-labeled Saccharibacteria provides high spatiotemporal resolution of phenomena accompanying epibiotic growth, and a transposon-insertion sequencing (Tn-seq) genome-wide screen reveals the contribution of enigmatic Saccharibacterial genes to growth on their hosts. Finally, we leverage metagenomic data to provide cutting-edge protein structure-based bioinformatic resources that support the strain Southlakia epibionticum and its corresponding host, Actinomyces israelii, as a model system for unlocking the molecular underpinnings of the epibiotic lifestyle.
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Affiliation(s)
- Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Larry A Gallagher
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Pia A Andrade
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Andi Liu
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | - Kevin J Cutler
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | | | - Yaqiao Li
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Matthew C Radey
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Jeffrey S McLean
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98109, USA
| | | | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98109, USA; Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA 98195, USA.
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4
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Dresen M, Valentin-Weigand P, Berhanu Weldearegay Y. Role of Metabolic Adaptation of Streptococcus suis to Host Niches in Bacterial Fitness and Virulence. Pathogens 2023; 12:pathogens12040541. [PMID: 37111427 PMCID: PMC10144218 DOI: 10.3390/pathogens12040541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Streptococcus suis, both a common colonizer of the porcine upper respiratory tract and an invasive pig pathogen, successfully adapts to different host environments encountered during infection. Whereas the initial infection mainly occurs via the respiratory tract, in a second step, the pathogen can breach the epithelial barrier and disseminate within the whole body. Thereby, the pathogen reaches other organs such as the heart, the joints, or the brain. In this review, we focus on the role of S. suis metabolism for adaptation to these different in vivo host niches to encounter changes in nutrient availability, host defense mechanisms and competing microbiota. Furthermore, we highlight the close link between S. suis metabolism and virulence. Mutants deficient in metabolic regulators often show an attenuation in infection experiments possibly due to downregulation of virulence factors, reduced resistance to nutritive or oxidative stress and to phagocytic activity. Finally, metabolic pathways as potential targets for new therapeutic strategies are discussed. As antimicrobial resistance in S. suis isolates has increased over the last years, the development of new antibiotics is of utmost importance to successfully fight infections in the future.
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Affiliation(s)
- Muriel Dresen
- Institute for Microbiology, University of Veterinary Medicine Hannover, 30173 Hannover, Germany
| | - Peter Valentin-Weigand
- Institute for Microbiology, University of Veterinary Medicine Hannover, 30173 Hannover, Germany
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He L, Tang W, Huang L, Zhou W, Huang S, Zou L, Yuan L, Men D, Chen S, Hu Y. Rational design of a genome-based insulated system in Escherichia coli facilitates heterologous uricase expression for hyperuricemia treatment. Bioeng Transl Med 2023; 8:e10449. [PMID: 36925686 PMCID: PMC10013758 DOI: 10.1002/btm2.10449] [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: 06/23/2022] [Revised: 09/18/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Hyperuricemia is a prevalent disease worldwide that is characterized by elevated urate levels in the blood owing to purine metabolic disorders, which can result in gout and comorbidities. To facilitate the treatment of hyperuricemia through the uricolysis, we engineered a probiotic Escherichia coli Nissle 1917 (EcN) named EcN C6 by inserting an FtsP-uricase cassette into an "insulated site" located between the uspG and ahpF genes. Expression of FtsP-uricase in this insulated region did not influence the probiotic properties or global gene transcription of EcN but strongly increased the enzymatic activity for urate degeneration, suggesting that the genome-based insulated system is an ideal strategy for EcN modification. Oral administration of EcN C6 successfully alleviated hyperuricemia, related symptoms and gut microbiota in a purine-rich food-induced hyperuricemia rat model and a uox-knockout mouse model. Together, our study provides an insulated site for heterologous gene expression in EcN strain and a recombinant EcN C6 strain as a safe and effective therapeutic candidate for hyperuricemia treatment.
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Affiliation(s)
- Lina He
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Wei Tang
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China
| | - Ling Huang
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Wei Zhou
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Shaojia Huang
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Linxuan Zou
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Lisha Yuan
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Dong Men
- State Key Laboratory of Virology Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China
| | - Shiyun Chen
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China
| | - Yangbo Hu
- State Key Laboratory of Virology Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,Hubei Jiangxia Laboratory Wuhan China
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Wu JF, Wei XP, Li JY, Sun WX. Recombinant Expression and Characterization of an Arginine Deiminase from Pseudomonas sp. LJY. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822060163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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7
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Dhankhar R, Kawatra A, Gupta V, Mohanty A, Gulati P. In silico and in vitro analysis of arginine deiminase from Pseudomonas furukawaii as a potential anticancer enzyme. 3 Biotech 2022; 12:220. [PMID: 35971334 PMCID: PMC9374873 DOI: 10.1007/s13205-022-03292-2] [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: 02/13/2022] [Accepted: 07/30/2022] [Indexed: 11/24/2022] Open
Abstract
Arginine deiminase (ADI), a promising anticancer enzyme from Mycoplasma hominis, is currently in phase III of clinical trials for the treatment of arginine auxotrophic tumors. However, it has been associated with several drawbacks in terms of low stability at human physiological conditions, high immunogenicity, hypersensitivity and systemic toxicity. In our previous work, Pseudomonas furukawaii 24 was identified as a potent producer of ADI with optimum activity under physiological conditions. In the present study, phylogenetic analysis of microbial ADIs indicated P. furukawaii ADI (PfADI) to be closely related to experimentally characterized ADIs of Pseudomonas sp. with proven anticancer activity. Immunoinformatics analysis was performed indicating lower immunogenicity of PfADI than MhADI (M. hominis ADI) both in terms of number of linear and conformational B-cell epitopes and T-cell epitope density. Overall antigenicity and allergenicity of PfADI was also lower as compared to MhADI, suggesting the applicability of PfADI as an alternative anticancer biotherapeutic. Hence, in vitro experiments were performed in which the ADI coding arcA gene of P. furukawaii was cloned and expressed in E. coli BL21. Recombinant ADI of P. furukawaii was purified, characterized and its anticancer activity was assessed. The enzyme was stable at human physiological conditions (pH 7 and 37 °C) with Km of 1.90 mM. PfADI was found to effectively inhibit the HepG2 cells with an IC50 value of 0.1950 IU/ml. Therefore, the current in silico and in vitro studies establish PfADI as a potential anticancer drug candidate with improved efficacy and low immunogenicity. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03292-2.
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Affiliation(s)
- Rakhi Dhankhar
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana India
| | - Anubhuti Kawatra
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana India
| | - Vatika Gupta
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana India
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Aparajita Mohanty
- Bioinformatics Infrastructure Facility, Gargi College, University of Delhi, New Delhi, India
| | - Pooja Gulati
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana India
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Subspecies Classification and Comparative Genomic Analysis of Lactobacillus kefiranofaciens HL1 and M1 for Potential Niche-Specific Genes and Pathways. Microorganisms 2022; 10:microorganisms10081637. [PMID: 36014054 PMCID: PMC9415760 DOI: 10.3390/microorganisms10081637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as Lactobacillus kefiranofaciens. The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different L. kefiranofaciens strains, but also the potential niche-specific genes and pathways among the L. kefiranofaciens strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as L. kefiranofaciens subsp. kefirgranum. According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the L. kefiranofaciens subsp. Kefirgranum genomes. Three unique genes (epsI, epsJ, and epsK) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism (glg) operon in the L. kefiranofaciens strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.
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Tikhomirova A, Zilm PS, Trappetti C, Paton JC, Kidd SP. The central role of arginine in Haemophilus influenzae survival in a polymicrobial environment with Streptococcus pneumoniae and Moraxella catarrhalis. PLoS One 2022; 17:e0271912. [PMID: 35877653 PMCID: PMC9312370 DOI: 10.1371/journal.pone.0271912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/08/2022] [Indexed: 11/18/2022] Open
Abstract
Haemophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis are bacterial species which frequently co-colonise the nasopharynx, but can also transit to the middle ear to cause otitis media. Chronic otitis media is often associated with a polymicrobial infection by these bacteria. However, despite being present in polymicrobial infections, the molecular interactions between these bacterial species remain poorly understood. We have previously reported competitive interactions driven by pH and growth phase between H. influenzae and S. pneumoniae. In this study, we have revealed competitive interactions between the three otopathogens, which resulted in reduction of H. influenzae viability in co-culture with S. pneumoniae and in triple-species culture. Transcriptomic analysis by mRNA sequencing identified a central role of arginine in mediating these interactions. Arginine supplementation was able to increase H. influenzae survival in a dual-species environment with S. pneumoniae, and in a triple-species environment. Arginine was used by H. influenzae for ATP production, and levels of ATP generated in dual- and triple-species co-culture at early stages of growth were significantly higher than the combined ATP levels of single-species cultures. These results indicate a central role for arginine-mediated ATP production by H. influenzae in the polymicrobial community.
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Affiliation(s)
- Alexandra Tikhomirova
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - Peter S. Zilm
- Department of Oral Microbiology, School of Dentistry, University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Claudia Trappetti
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - James C. Paton
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - Stephen P. Kidd
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
- Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, Australia
- * E-mail:
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Acidic Neutralization by Indigenous Bacteria Isolated from Abandoned Mine Areas. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soil acidification has been a serious problem in abandoned mine areas, and could be exacerbated by acid deposition with the release of mine wastes. In this study, three different indigenous bacterial consortia were isolated from abandoned mines in South Korea, from which the potential for acid neutralization of microorganisms was evaluated. They were all able to neutralize acidity within 24 h in the liquid nutrient medium. Moreover, a strong positive correlation (R = +0.922, p < 0.05) was established between the ammonium ion (NH4+) production yield and the resulting pH, indicating that NH4+ served as an important metabolite for biological neutralization. Serratialiquefaciens, Citrobacter youngae, Pseudescherichia vulneris, and Serratia grimesii had higher acid neutralization ability to generate NH4+ by the metabolism of nitrogen compounds such as carboxylation and urea hydrolysis. Therefore, acidic soils can be expected to be ameliorated by indigenous microorganisms through in situ biostimulation with the adequate introduction of nitrogenous substances into the soil environments.
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The arginine deaminase system plays distinct roles in Borrelia burgdorferi and Borrelia hermsii. PLoS Pathog 2022; 18:e1010370. [PMID: 35286343 PMCID: PMC8947608 DOI: 10.1371/journal.ppat.1010370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/24/2022] [Accepted: 02/14/2022] [Indexed: 11/23/2022] Open
Abstract
Borrelia species are amino acid auxotrophs that utilize di- and tri- peptides obtained through their oligopeptide transport system to supply amino acids for replicative growth during their enzootic cycles. However, Borrelia species from both the Lyme disease (LD) and relapsing fever (RF) groups harbor an amino acid transport and catabolism system, the Arginine Deiminase System (ADI), that could potentially augment intracellular L-arginine required for growth. RF spirochetes contain a “complete”, four gene ADI (arcA, B, D, and C) while LD spirochetes harbor arcA, B, and sometimes D but lack arcC (encoding carbamate kinase). In this study, we evaluated the role of the ADI system in bacterial survival and virulence and discovered important differences in RF and LD ADIs. Both in vitro and in a murine model of infection, B. hermsii cells significantly reduced extracellular L-arginine levels and that reduction was dependent on arginine deiminase expression. Conversely, B. burgdorferi did not reduce the concentration of L-arginine during in vitro growth experiments nor during infection of the mammalian host, suggesting a fundamental difference in the ability to directly utilize L-arginine compared to B. hermsii. Further experiments using a panel of mutants generated in both B. burgdorferi and B. hermsii, identified important differences in growth characteristics and ADI transcription and protein expression. We also found that the ADI system plays a key role in blood and spleen colonization in RF spirochetes. In this study we have identified divergent metabolic strategies in two closely related human pathogens, that ultimately impacts the host-pathogen interface during infection. Reports of tick-borne diseases have been steadily increasing in the US and the number of Lyme disease cases caused by B. burgdorferi have tripled since the late 1990’s. Although less common, cases of tick-borne relapsing fever, caused by B. hermsii and B. turicatae in the US, have increased as well. While transmitted by different ticks and maintained in unique enzootic cycles, the closely related spirochetes B. burgdorferi and B. hermsii share numerous genetic features including a truncated and streamlined capacity for metabolic activity. In this study we combine genetic and biochemical assays to define the role of the ADI in the infective cycles of B. burgdorferi and B. hermsii. When we compared B. burgdorferi and B. hermsii, we identified important differences in their respective ADI’s including operon arrangement, sensitivity to L-arginine and L-ornithine levels, as well as gene and protein expression. In addition, we show that arginine deiminase is required to reduce host L-arginine levels during murine infection with B. hermsii. This study provides new insights into the metabolic activities of two medically relevant spirochetes and highlights the dynamic nature of host-pathogen interactions.
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Exploration of the roles of spoilage bacteria in degrading grass carp proteins during chilled storage: A combined metagenomic and metabolomic approach. Food Res Int 2022; 152:110926. [DOI: 10.1016/j.foodres.2021.110926] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022]
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13
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Yi Z, Xie J. Assessment of spoilage potential and amino acids deamination & decarboxylation activities of Shewanella putrefaciens in bigeye tuna (Thunnus obesus). Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.113016] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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14
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Microbial arginine deiminase: A multifaceted green catalyst in biomedical sciences. Int J Biol Macromol 2022; 196:151-162. [PMID: 34920062 DOI: 10.1016/j.ijbiomac.2021.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/03/2021] [Accepted: 12/04/2021] [Indexed: 12/18/2022]
Abstract
Arginine deiminase is a well-recognized guanidino-modifying hydrolase that catalyzes the conversion of L-arginine to citrulline and ammonia. Their biopotential to regress tumors via amino acid deprivation therapy (AADT) has been well established. PEGylated formulation of recombinant Mycoplasma ADI is in the last-phase clinical trials against various arginine-auxotrophic cancers like hepatocellular carcinoma, melanoma, and mesothelioma. Recently, ADIs have attained immense importance in several other biomedical applications, namely treatment of Alzheimer's, as an antiviral drug, bioproduction of nutraceutical L-citrulline and bio-analytics involving L-arginine detection. Considering the wide applications of this biodrug, the demand for ADI is expected to escalate several-fold in the coming years. However, the sustainable production aspects of the enzyme with improved pharmacokinetics is still limited, creating bottlenecks for effective biopharmaceutical development. To circumvent the lacunae in enzyme production with appropriate paradigms of 'quality-by-design' an explicit overview of its properties with 'biobetter' formulations strategies are required. Present review provides an insight into all the potential biomedical applications of ADI along with the improvements required for its reach to clinics. Recent research advances with special emphasis on the development of ADI as a 'biobetter' enzyme have also been comprehensively elaborated.
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15
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Zhou K, Zhang X, Li B, Shen C, Sun YM, Yang J, Xu ZL. Citrulline Accumulation Mechanism of Pediococcus acidilactici and Weissella confusa in Soy Sauce and the Effects of Phenolic Compound on Citrulline Accumulation. Front Microbiol 2021; 12:757542. [PMID: 34925267 PMCID: PMC8678507 DOI: 10.3389/fmicb.2021.757542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/19/2021] [Indexed: 11/23/2022] Open
Abstract
Citrulline is one of the major precursors of ethyl carbamate in soy sauce, and the accumulation of citrulline is attributed to the metabolism of arginine by bacteria with the arginine deiminase (ADI) pathway. However, key strains and factors affecting citrulline accumulation are not yet clear. In this study, two key strains of Pediococcus acidilactici and Weissella confusa were isolated from soy sauce moromi, and the regularity of citrulline formation was studied. Results showed that the conversion rates from arginine to citrulline (A/C rate) and the citrulline accumulation ability of W. confusa and P. acidilactici significantly increased in the presence of different concentrations of NaCl, indicating that salt stress was the main factor for citrulline accumulation. The inconsistent expression of arc genes by salt stress was the reason for citrulline accumulation for P. acidilactici, but for W. confusa, it may be due to the influence of arginine/citrulline on the transportation system: the intracellular citrulline could neither transport to extracellular space nor convert into ornithine. Environmental factors greatly influenced citrulline accumulation of the two key bacteria; A/C rate and citrulline formation in both strains decreased at low temperature (15°C) under high salt stress, but opposite effects were observed for the two key strains under anaerobic light condition. Moreover, quercetin and gallic acid significantly decreased the A/C rate and citrulline accumulation ability of the two key strains. The optimal quercetin and gallic acid as suggested by simulation experiment were 100 and 10 mg/l, respectively, and the lowest A/C rate of 28.4% and citrulline level of 1326.7 mg/l were achieved in the simulation system. This study explored the main factors for citrulline formation by the two key strains and proposed a targeted way to control citrulline in soy sauce.
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Affiliation(s)
- Kai Zhou
- Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang, China.,Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou, China.,Department of Production-Learning-Research, Shenzhen Total-Test Technology Co., Ltd., Shenzhen, China
| | - Xiao Zhang
- Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang, China
| | - Bingyong Li
- Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang, China
| | - Chaoqun Shen
- Department of Production-Learning-Research, Shenzhen Total-Test Technology Co., Ltd., Shenzhen, China
| | - Yuan-Ming Sun
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Jianyuan Yang
- Institute of Jiangxi Oil-Tea Camellia, Jiujiang University, Jiujiang, China
| | - Zhen-Lin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou, China
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16
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Han S, Van Treuren W, Fischer CR, Merrill BD, DeFelice BC, Sanchez JM, Higginbottom SK, Guthrie L, Fall LA, Dodd D, Fischbach MA, Sonnenburg JL. A metabolomics pipeline for the mechanistic interrogation of the gut microbiome. Nature 2021; 595:415-420. [PMID: 34262212 PMCID: PMC8939302 DOI: 10.1038/s41586-021-03707-9] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 06/08/2021] [Indexed: 02/06/2023]
Abstract
Gut microorganisms modulate host phenotypes and are associated with numerous health effects in humans, ranging from host responses to cancer immunotherapy to metabolic disease and obesity. However, difficulty in accurate and high-throughput functional analysis of human gut microorganisms has hindered efforts to define mechanistic connections between individual microbial strains and host phenotypes. One key way in which the gut microbiome influences host physiology is through the production of small molecules1-3, yet progress in elucidating this chemical interplay has been hindered by limited tools calibrated to detect the products of anaerobic biochemistry in the gut. Here we construct a microbiome-focused, integrated mass-spectrometry pipeline to accelerate the identification of microbiota-dependent metabolites in diverse sample types. We report the metabolic profiles of 178 gut microorganism strains using our library of 833 metabolites. Using this metabolomics resource, we establish deviations in the relationships between phylogeny and metabolism, use machine learning to discover a previously undescribed type of metabolism in Bacteroides, and reveal candidate biochemical pathways using comparative genomics. Microbiota-dependent metabolites can be detected in diverse biological fluids from gnotobiotic and conventionally colonized mice and traced back to the corresponding metabolomic profiles of cultured bacteria. Collectively, our microbiome-focused metabolomics pipeline and interactive metabolomics profile explorer are a powerful tool for characterizing microorganisms and interactions between microorganisms and their host.
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Affiliation(s)
- Shuo Han
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Will Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Microbiology and Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Curt R. Fischer
- ChEM-H, Stanford University, Stanford, CA, USA,Chan-Zuckerburg Biohub, San Francisco, CA, USA
| | - Bryan D. Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Microbiology and Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Leah Guthrie
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lalla A. Fall
- ChEM-H, Stanford University, Stanford, CA, USA,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA,Address correspondence to: , ,
| | - Michael A. Fischbach
- Chan-Zuckerburg Biohub, San Francisco, CA, USA,Department of Bioengineering, Stanford University, Stanford, CA, USA,Address correspondence to: , ,
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Chan-Zuckerburg Biohub, San Francisco, CA, USA,Center for Human Microbiome Studies, Stanford, CA, USA,Address correspondence to: , ,
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17
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Costantini PE, Firrincieli A, Fedi S, Parolin C, Viti C, Cappelletti M, Vitali B. Insight into phenotypic and genotypic differences between vaginal Lactobacillus crispatus BC5 and Lactobacillus gasseri BC12 to unravel nutritional and stress factors influencing their metabolic activity. Microb Genom 2021; 7. [PMID: 34096840 PMCID: PMC8461478 DOI: 10.1099/mgen.0.000575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The vaginal microbiota, normally characterized by lactobacilli presence, is crucial for vaginal health. Members belonging to L. crispatus and L. gasseri species exert crucial protective functions against pathogens, although a total comprehension of factors that influence their dominance in healthy women is still lacking. Here we investigated the complete genome sequence and comprehensive phenotypic profile of L. crispatus strain BC5 and L. gasseri strain BC12, two vaginal strains featured by anti-bacterial and anti-viral activities. Phenotype microarray (PM) results revealed an improved capacity of BC5 to utilize different carbon sources as compared to BC12, although some specific carbon sources that can be associated to the human diet were only metabolized by BC12, i.e. uridine, amygdalin, tagatose. Additionally, the two strains were mostly distinct in the capacity to utilize the nitrogen sources under analysis. On the other hand, BC12 showed tolerance/resistance towards twice the number of stressors (i.e. antibiotics, toxic metals etc.) with respect to BC5. The divergent phenotypes observed in PM were supported by the identification in either BC5 or BC12 of specific genetic determinants that were found to be part of the core genome of each species. The PM results in combination with comparative genome data provide insights into the possible environmental factors and genetic traits supporting the predominance of either L. crispatus BC5 or L. gasseri BC12 in the vaginal niche, giving also indications for metabolic predictions at the species level.
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Affiliation(s)
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Carlo Viti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
| | - Beatrice Vitali
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
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18
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Thomas SC, Payne D, Tamadonfar KO, Seymour CO, Jiao JY, Murugapiran SK, Lai D, Lau R, Bowen BP, Silva LP, Louie KB, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Chen IM, Stamatis D, Reddy TBK, O'Malley R, Daum C, Shapiro N, Ivanova N, Kyrpides NC, Woyke T, Eloe-Fadrosh E, Hamilton TL, Dijkstra P, Dodsworth JA, Northen TR, Li WJ, Hedlund BP. Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan. Front Microbiol 2021; 12:632731. [PMID: 34017316 PMCID: PMC8129789 DOI: 10.3389/fmicb.2021.632731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/02/2021] [Indexed: 01/21/2023] Open
Abstract
Thermoflexus hugenholtzii JAD2T, the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2T using 13C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.
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Affiliation(s)
- Scott C Thomas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Devon Payne
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Kevin O Tamadonfar
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Cale O Seymour
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Jian-Yu Jiao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Senthil K Murugapiran
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Department of Plant and Microbial Biology, The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Dengxun Lai
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Rebecca Lau
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Katherine B Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcel Huntemann
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alicia Clum
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alex Spunde
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Manoj Pillay
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Krishnaveni Palaniappan
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Neha Varghese
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Mikhailova
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - I-Min Chen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Dimitrios Stamatis
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - T B K Reddy
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ronan O'Malley
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Chris Daum
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicole Shapiro
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Ivanova
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nikos C Kyrpides
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Emiley Eloe-Fadrosh
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, The BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Paul Dijkstra
- Department of Biological Sciences, Center of Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, United States
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA, United States
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
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19
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Jung S, An H, Lee JH. Red pepper powder is an essential factor for ornithine production in kimchi fermentation. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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20
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Afshari R, Pillidge CJ, Dias DA, Osborn AM, Gill H. Microbiota and Metabolite Profiling Combined With Integrative Analysis for Differentiating Cheeses of Varying Ripening Ages. Front Microbiol 2020; 11:592060. [PMID: 33324371 PMCID: PMC7726019 DOI: 10.3389/fmicb.2020.592060] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/03/2020] [Indexed: 11/30/2022] Open
Abstract
Cheese maturation and flavor development results from complex interactions between milk substrates, cheese microbiota and their metabolites. In this study, bacterial 16S rRNA-gene sequencing, untargeted metabolomics (gas chromatography-mass spectrometry) and data integration analyses were used to characterize and differentiate commercial Cheddar cheeses of varying maturity made by the same and different manufacturers. Microbiota and metabolite compositions varied between cheeses of different ages and brands, and could be used to distinguish the cheeses. Individual amino acids and carboxylic acids were positively correlated with the ripening age for some brands. Integration and Random Forest analyses revealed numerous associations between specific bacteria and metabolites including a previously undescribed positive correlation between Thermus and phenylalanine and a negative correlation between Streptococcus and cholesterol. Together these results suggest that multi-omics analyses has the potential to be used for better understanding the relationships between cheese microbiota and metabolites during ripening and for discovering biomarkers for validating cheese age and brand authenticity.
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Affiliation(s)
- Roya Afshari
- School of Science, RMIT University, Bundoora, VIC, Australia
| | | | - Daniel A. Dias
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - A. Mark Osborn
- School of Science, RMIT University, Bundoora, VIC, Australia
| | - Harsharn Gill
- School of Science, RMIT University, Bundoora, VIC, Australia
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21
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Lin J, Luo X, Gänzle MG, Luo L. Characterization of the two nonidentical ArgR regulators of Tetragenococcus halophilus and their regulatory effects on arginine metabolism. Appl Microbiol Biotechnol 2020; 104:8775-8787. [PMID: 32880693 DOI: 10.1007/s00253-020-10868-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/06/2020] [Accepted: 08/26/2020] [Indexed: 11/25/2022]
Abstract
The halophilic lactic acid bacterium Tetragenococcus halophilus has been widely used in high-salinity fermentation processes of food. Previous studies have indicated that the catabolism of arginine may contribute to the osmotic stress adaptation of T. halophilus. Unusually, in the chromosome of T. halophilus, preceding the arginine deiminase (ADI) operon, locate two co-transcribed genes, both encoding an ArgR regulator; similar structure was rarely found and the roles of the regulators have not been demonstrated. In the current study, regulatory roles of these two nonidentical ArgR regulators on the arginine metabolism of T. halophilus were investigated. The results show that these two regulators play different roles in arginine metabolism, ArgR1 acts as a negative regulator of the ADI pathway by binding to the promoter sequences and repressing the transcription of genes, and the addition of arginine or hyper-osmotic stress conditions can abolish the ArgR1 repression, whereas ArgR2 negatively regulates the genes involved in arginine biosynthesis. Our study found that despite the commonly known roles of the ArgR regulators as the activator of arginine catabolism and the repressor of arginine biosynthesis, which are found in most studied bacteria possessed one ArgR regulator, the two nonidentical ArgR regulators of T. halophilus both act as repressors, and the repression by which is regulated when sensing changes of environments. By revealing the regulation of arginine metabolism, the current study provides molecular insights and potential tools for future applications of halophiles in biotechnology. KEY POINTS: • The expression of the ADI pathway of T. halophilus is regulated by carbon sources and osmotic stress. • The arginine metabolism process of T. halophilus is fine-tuned by the two ArgR regulators. • The ADI pathway may contribute to the osmotic stress adaptation by generating more energy and accumulating citrulline which acts as compatible solute.
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Affiliation(s)
- Jieting Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Xiaotong Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta, T6G 2P5, Canada
| | - Lixin Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
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22
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Zhuang S, Liu X, Li Y, Zhang L, Hong H, Liu J, Luo Y. Biochemical changes and amino acid deamination & decarboxylation activities of spoilage microbiota in chill-stored grass carp (Ctenopharyngodon idella) fillets. Food Chem 2020; 336:127683. [PMID: 32771900 DOI: 10.1016/j.foodchem.2020.127683] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/11/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022]
Abstract
This study aimed to reveal amino acid deamination and decarboxylation activities of spoilage microbiota in chill-stored grass carp fillets. Results showed that microbial deamination activities of umami/sweet-taste amino acids were higher than that of bitter-taste amino acids. The total deamination activity of tested amino acids decreased during the late period of storage, which inhibited the increase of ammonia in fish flesh. Microbial decarboxylation activity of ornithine was much higher than lysine and histidine, which was consistent with the rapid increase of putrescine in fish fillets. Meanwhile, putrescine could be produced in large quantities through arginine deiminase pathway of spoilage bacteria. Glucose utilization by spoilage microbiota was active during the late period of storage, which was consistent with the rapid consumption of lactate and total sugar in fish flesh. Overall, results of this study could be beneficial for revealing fish spoilage mechanisms and providing theoretical guidance for developing fish preservation technologies.
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Affiliation(s)
- Shuai Zhuang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaochang Liu
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yan Li
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longteng Zhang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hui Hong
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jun Liu
- National Research and Development Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| | - Yongkang Luo
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Research and Development Center for Freshwater Fish Processing (Beijing), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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23
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Mun SY, Chang HC. Characterization of Weissella koreensis SK Isolated from Kimchi Fermented at Low Temperature (around 0 °C) Based on Complete Genome Sequence and Corresponding Phenotype. Microorganisms 2020; 8:E1147. [PMID: 32751267 PMCID: PMC7464874 DOI: 10.3390/microorganisms8081147] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 01/12/2023] Open
Abstract
This study identified lactic acid bacteria (LAB) that play a major role in kimchi fermented at low temperature, and investigated the safety and functionality of the LAB via biologic and genomic analyses for its potential use as a starter culture or probiotic. Fifty LAB were isolated from 45 kimchi samples fermented at -1.5~0 °C for 2~3 months. Weissella koreensis strains were determined as the dominant LAB in all kimchi samples. One strain, W. koreensis SK, was selected and its phenotypic and genomic features characterized. The complete genome of W. koreensis SK contains one circular chromosome and plasmid. W. koreensis SK grew well under mesophilic and psychrophilic conditions. W. koreensis SK was found to ferment several carbohydrates and utilize an alternative carbon source, the amino acid arginine, to obtain energy. Supplementation with arginine improved cell growth and resulted in high production of ornithine. The arginine deiminase pathway of W. koreensis SK was encoded in a cluster of four genes (arcA-arcB-arcD-arcC). No virulence traits were identified in the genomic and phenotypic analyses. The results indicate that W. koreensis SK may be a promising starter culture for fermented vegetables or fruits at low temperature as well as a probiotic candidate.
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Affiliation(s)
| | - Hae Choon Chang
- Department of Food and Nutrition, Kimchi Research Center, Chosun University, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Korea;
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24
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Pols T, Singh S, Deelman-Driessen C, Gaastra BF, Poolman B. Enzymology of the pathway for ATP production by arginine breakdown. FEBS J 2020; 288:293-309. [PMID: 32306469 PMCID: PMC7818446 DOI: 10.1111/febs.15337] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 01/02/2023]
Abstract
In cells, the breakdown of arginine to ornithine and ammonium ion plus carbon dioxide is coupled to the generation of metabolic energy in the form of ATP. The arginine breakdown pathway is minimally composed of arginine deiminase, ornithine transcarbamoylase, carbamate kinase, and an arginine/ornithine antiporter; ammonia and carbon dioxide most likely diffuse passively across the membrane. The genes for the enzymes and transporter have been cloned and expressed, and the proteins have been purified from Lactococcus lactis IL1403 and incorporated into lipid vesicles for sustained production of ATP. Here, we study the kinetic parameters and biochemical properties of the individual enzymes and the antiporter, and we determine how the physicochemical conditions, effector composition, and effector concentration affect the enzymes. We report the KM and VMAX values for catalysis and the native oligomeric state of all proteins, and we measured the effect of pathway intermediates, pH, temperature, freeze-thaw cycles, and salts on the activity of the cytosolic enzymes. We also present data on the protein-to-lipid ratio and lipid composition dependence of the antiporter.
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Affiliation(s)
- Tjeerd Pols
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Shubham Singh
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Cecile Deelman-Driessen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Bauke F Gaastra
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, The Netherlands
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Abdollahi S, Morowvat MH, Savardashtaki A, Irajie C, Najafipour S, Zarei M, Ghasemi Y. Amino Acids Sequence-based Analysis of Arginine Deiminase from Different Prokaryotic Organisms: An In Silico Approach. Recent Pat Biotechnol 2020; 14:235-246. [PMID: 32208128 DOI: 10.2174/1872208314666200324114441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/31/2020] [Accepted: 03/11/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Arginine deiminase is a bacterial enzyme, which degrades L-arginine. Some human cancers such as hepatocellular carcinoma (HCC) and melanoma are auxotrophic for arginine. Therefore, PEGylated arginine deiminase (ADI-PEG20) is a good anticancer candidate with antitumor effects. It causes local depletion of L-arginine and growth inhibition in arginineauxotrophic tumor cells. The FDA and EMA have granted orphan status to this drug. Some recently published patents have dealt with this enzyme or its PEGylated form. OBJECTIVE Due to increasing attention to it, we aimed to evaluate and compare 30 arginine deiminase proteins from different bacterial species through in silico analysis. METHODS The exploited analyses included the investigation of physicochemical properties, multiple sequence alignment (MSA), motif, superfamily, phylogenetic and 3D comparative analyses of arginine deiminase proteins thorough various bioinformatics tools. RESULTS The most abundant amino acid in the arginine deiminase proteins is leucine (10.13%) while the least amino acid ratio is cysteine (0.98%). Multiple sequence alignment showed 47 conserved patterns between 30 arginine deiminase amino acid sequences. The results of sequence homology among 30 different groups of arginine deiminase enzymes revealed that all the studied sequences located in amidinotransferase superfamily. Based on the phylogenetic analysis, two major clusters were identified. Considering the results of various in silico studies; we selected the five best candidates for further investigations. The 3D structures of the best five arginine deiminase proteins were generated by the I-TASSER server and PyMOL. The RAMPAGE analysis revealed that 81.4%-91.4%, of the selected sequences, were located in the favored region of arginine deiminase proteins. CONCLUSION The results of this study shed light on the basic physicochemical properties of thirty major arginine deiminase sequences. The obtained data could be employed for further in vivo and clinical studies and also for developing the related therapeutic enzymes.
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Affiliation(s)
- Sara Abdollahi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, P.O. Box 71348-14366, Shiraz, Iran
| | - Mohammad H Morowvat
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, P.O. Box 71348-14366, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, P.O. Box 71348-14366, Shiraz, Iran
| | - Cambyz Irajie
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, P.O. Box 71348-14366, Shiraz, Iran
| | - Sohrab Najafipour
- Department of Microbiology, School of Medicine, Fasa University of Medical Sciences, P.O. Box 74616-86688, Fasa, Iran
| | - Mahboubeh Zarei
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, P.O. Box 71468-64685, Shiraz, Iran
| | - Younes Ghasemi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, P.O. Box 71348-14366, Shiraz, Iran
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Zarei M, Rahbar MR, Nezafat N, Negahdaripour M, Morowvat MH, Ghasemi Y. Computational Analysis of Arginine Deiminase Sequences to Provide a Guideline for Protein Engineering. CURR PROTEOMICS 2020. [DOI: 10.2174/1570164616666190619111852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background:Arginine deiminase of Mycoplasma hominis, an arginine catabolizing enzyme, is currently in clinical trial for the treatment of arginine auxotrophic cancers. However, some drawbacks such as instability and antigenicity have limited its application as a protein drug. Arginine Deiminase (ADI) belongs to the guanidino-group modifying enzyme superfamily. Despite differences in the primary amino acid sequences of various members of this superfamily, the folding and secondary structures are conserved in all members. Despite structural similarities, ADIs in various species have different levels of catalytic activity and physicochemical properties due to the differences in their primary amino acid sequences. Therefore, investigating and comparing sequences between different ADI producing bacterial strains could be helpful in the rational engineering of ADI.Objective:In the current research, we used an in-silico approach to characterize and classify the available reviewed protein sequences of ADI.Results:102 ADI sequences from SwissProt database were extracted. Subsequently, based on clustering analyses, the sequence sets were divided into five distinct groups. Different physicochemical properties, solubility, and antigenicity of the enzymes were determined. Some ADI sequences were introduced as well-suited candidates for protein engineering; Lactobacillus fermentum ADI for low pI value, Mycobacterium avium ADI for high aliphatic index, Bacillus licheniformis ADI for low GRAVY index, Bradyrhizobium diazoefficiens ADI for low antigenicity and high stability index, and among Mycoplasma ADIs, Mycoplasma arthritidis ADI for high stability and aliphatic index, and Mycoplasma capricolum for low antigenicity.
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Affiliation(s)
- Mahboubeh Zarei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Matoba Y, Uda N, Kudo M, Sugiyama M. Cyclization mechanism catalyzed by an ATP-grasp enzyme essential for d-cycloserine biosynthesis. FEBS J 2019; 287:2763-2778. [PMID: 31793174 DOI: 10.1111/febs.15163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/20/2019] [Accepted: 12/02/2019] [Indexed: 11/26/2022]
Abstract
In the biosynthetic pathway of an antitubercular antibiotic d-cycloserine (d-CS), O-ureido-d-serine (d-OUS) is converted to d-CS. We have previously demonstrated that DcsG, classified into the ATP-grasp superfamily enzyme, catalyzes the ring formation to generate d-CS, which is accompanied by the cleavage of a bond in the urea moiety of d-OUS to remove a carbamoyl group. Although the general ATP-grasp enzymes catalyze an ATP-dependent ligation reaction between two substrates, DcsG catalyzes specifically the generation of an intramolecular covalent bond. In the present study, cyanate was found in the reaction mixture, suggesting that carbamoyl group is eliminated as an isocyanic acid during the reaction. By the crystallographic and mutational investigations of DcsG, we anticipate the residues necessary for the binding of d-OUS. An acylphosphate intermediate must be bound at the narrow pocket of DcsG in a folded conformation, inducing the bond cleavage and the new bond formation to generate cyanate and d-CS, respectively. DATABASE: Structural data are available in Protein Data Bank database under the accession number 6JIL.
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Affiliation(s)
- Yasuyuki Matoba
- Faculty of Pharmacy, Yasuda Women's University, Hiroshima, Japan
| | - Narutoshi Uda
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan
| | - Mako Kudo
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan
| | - Masanori Sugiyama
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan
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Beck MH, Flaiz M, Bengelsdorf FR, Dürre P. Induced heterologous expression of the arginine deiminase pathway promotes growth advantages in the strict anaerobe Acetobacterium woodii. Appl Microbiol Biotechnol 2019; 104:687-699. [DOI: 10.1007/s00253-019-10248-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/30/2019] [Accepted: 11/05/2019] [Indexed: 01/12/2023]
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Rópolo AS, Feliziani C, Touz MC. Unusual proteins in Giardia duodenalis and their role in survival. ADVANCES IN PARASITOLOGY 2019; 106:1-50. [PMID: 31630755 DOI: 10.1016/bs.apar.2019.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The capacity of the parasite Giardia duodenalis to perform complex functions with minimal amounts of proteins and organelles has attracted increasing numbers of scientists worldwide, trying to explain how this parasite adapts to internal and external changes to survive. One explanation could be that G. duodenalis evolved from a structurally complex ancestor by reductive evolution, resulting in adaptation to its parasitic lifestyle. Reductive evolution involves the loss of genes, organelles, and functions that commonly occur in many parasites, by which the host renders some structures and functions redundant. However, there is increasing data that Giardia possesses proteins able to perform more than one function. During recent decades, the concept of moonlighting was described for multitasking proteins, which involves only proteins with an extra independent function(s). In this chapter, we provide an overview of unusual proteins in Giardia that present multifunctional properties depending on the location and/or parasite requirement. We also discuss experimental evidence that may allow some giardial proteins to be classified as moonlighting proteins by examining the properties of moonlighting proteins in general. Up to date, Giardia does not seem to require the numerous redundant proteins present in other organisms to accomplish its normal functions, and thus this parasite may be an appropriate model for understanding different aspects of moonlighting proteins, which may be helpful in the design of drug targets.
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Affiliation(s)
- Andrea S Rópolo
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Constanza Feliziani
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María C Touz
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina.
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Abstract
Dental caries is closely related to a dysbiosis of the microbial consortia of supragingival oral biofilms driven by a sugar-frequent and acidic-pH environment. The pH is a key factor affecting the homeostasis of supragingival biofilms seen in health. There is increasing interest on the ecological dynamics of the oral microbiome and how a dysbiotic microbiota can be successfully replaced by health-beneficial flora. The concept of preventing the microbial dysbiosis related to caries through modulation of sugar intake and pH has fully emerged.
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Affiliation(s)
- Marcelle M Nascimento
- Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, University of Florida, 1395 Center Drive, Room D9-6, PO Box 100415, Gainesville, FL 32610-0415, USA.
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31
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Nelkner J, Tejerizo GT, Hassa J, Lin TW, Witte J, Verwaaijen B, Winkler A, Bunk B, Spröer C, Overmann J, Grosch R, Pühler A, Schlüter AA. Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics. Genes (Basel) 2019; 10:E601. [PMID: 31405015 PMCID: PMC6722718 DOI: 10.3390/genes10080601] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 01/17/2023] Open
Abstract
The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.
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Affiliation(s)
- Johanna Nelkner
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Gonzalo Torres Tejerizo
- Facultad de Ciencias Exactas, Departamento de Ciencias Biologicas, IBBM, Universidad Nacional de La Plata, Calle 115 y 47, 1900 La Plata, Argentina
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Timo Wentong Lin
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Julian Witte
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Bart Verwaaijen
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Boyke Bunk
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Rita Grosch
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - And Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
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32
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Regulation of arginine biosynthesis, catabolism and transport in Escherichia coli. Amino Acids 2019; 51:1103-1127. [DOI: 10.1007/s00726-019-02757-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
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Starikova EA, Golovin AS, Vasilyev KA, Karaseva AB, Serebriakova MK, Sokolov AV, Kudryavtsev IV, Burova LA, Voynova IV, Suvorov AN, Vasilyev VB, Freidlin IS. Role of arginine deiminase in thymic atrophy during experimental Streptococcus pyogenes infection. Scand J Immunol 2019; 89:e12734. [PMID: 30471128 DOI: 10.1111/sji.12734] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/11/2018] [Accepted: 11/18/2018] [Indexed: 01/08/2023]
Abstract
Expression of gene of arginine deiminase (AD) allows adaptation of Streptococcus pyogenes to adverse environmental conditions. AD activity can lead to L-arginine deficiency in the host cells' microenvironment. Bioavailability of L-arginine is an important factor regulating the functions of the immune cells in mammals. By introducing a mutation into S pyogenes M46-16, we obtained a strain with inactivated arcA/sagp gene (M49-16 delArcA), deficient in AD. This allowed elucidating the function of AD in pathogenesis of streptococcal infection. The virulence of the parental and mutant strains was examined in a murine model of subcutaneous streptococcal infection. L-arginine concentration in the plasma of mice infected with S pyogenes M49-16 delArcA remained unchanged in course of the entire experiment. At the same time mice infected with S pyogenes M49-16 demonstrated gradual diminution of L-arginine concentration in the blood plasma, which might be due to the activity of streptococcal AD. Mice infected with S pyogenes M49-16 delArcA demonstrated less intensive bacterial growth in the primary foci and less pronounced bacterial dissemination as compared with animals infected with the parental strain S pyogenes M46-16. Similarly, thymus involution, alterations in apoptosis, thymocyte subsets and Treg cells differentiation were less pronounced in mice infected with S pyogenes M49-16 delArcA than in those infected with the parental strain. The results obtained showed that S pyogenes M49-16 delArcA, unable to produce AD, had reduced virulence in comparison with the parental S pyogenes M49-16 strain. AD is an important factor for the realization of the pathogenic potential of streptococci.
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Affiliation(s)
| | | | | | - Alena Borisovna Karaseva
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia
| | | | - Alexey Victorovich Sokolov
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia.,Saint-Petersburg State University, St. Petersburg, Russia
| | - Igor Vladimirovich Kudryavtsev
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia.,Far Eastern Federal University Vladivostok, Russia
| | | | - Irina Vitalyevna Voynova
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia
| | - Alexander Nikolaevich Suvorov
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia.,Saint-Petersburg State University, St. Petersburg, Russia
| | - Vadim Borisovich Vasilyev
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia.,Saint-Petersburg State University, St. Petersburg, Russia
| | - Irina Solomonovna Freidlin
- Federal State Budgetary Scientific Institution, Institute of Experimental Medicine, St. Petersburg, Russia.,Saint-Petersburg State University, St. Petersburg, Russia.,Pavlov First Saint-Petersburg State Medical University, St. Petersburg, Russia
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Zarei M, Rahbar MR, Morowvat MH, Nezafat N, Negahdaripour M, Berenjian A, Ghasemi Y. Arginine Deiminase: Current Understanding and Applications. Recent Pat Biotechnol 2019; 13:124-136. [PMID: 30569861 DOI: 10.2174/1872208313666181220121400] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/07/2018] [Accepted: 12/25/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Arginine deiminase (ADI), an arginine catabolizing enzyme, is considered as an anti-tumor agent for the treatment of arginine auxotrophic cancers. However, some obstacles limit its clinical applications. OBJECTIVE This review will summarize the clinical applications of ADI, from a brief history to its limitations, and will discuss the different ways to deal with the clinical limitations. METHOD The structure analysis, cloning, expression, protein engineering and applications of arginine deiminase enzyme have been explained in this review. CONCLUSION Recent patents on ADI are related to ADI engineering to increase its efficacy for clinical application. The intracellular delivery of ADI and combination therapy seem to be the future strategies in the treatment of arginine auxotrophic cancers. Applying ADIs with optimum features from different sources and or ADI engineering, are promising strategies to improve the clinical application of ADI.
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Affiliation(s)
- Mahboubeh Zarei
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Rahbar
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hossein Morowvat
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aydin Berenjian
- School of Engineering, Faculty of Science & Engineering, The University of Waikato, Hamilton, New Zealand
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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35
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The effect of starters with a functional arginine deiminase pathway on cheese ripening and quality. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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36
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Nakamura A, Ooga T, Matsumoto M. Intestinal luminal putrescine is produced by collective biosynthetic pathways of the commensal microbiome. Gut Microbes 2018; 10:159-171. [PMID: 30183487 PMCID: PMC6546329 DOI: 10.1080/19490976.2018.1494466] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The intestinal microbiome produces various metabolites that may harm or benefit the host. However, the production pathways of these metabolites have not been well characterised. The polyamines putrescine and spermidine required for physiological process are also produced by intestinal microbiome. The production and release of these polyamines by microbiome are poorly understood, though we have confirmed that intestinal bacteria produced putrescine from arginine. In this study, we characterised polyamine synthesis by analysing the collective metabolic functions of the intestinal microbiome. In particular, we analysed polyamines and their intermediates in faecal cultures, as well as the colonic contents of rats injected with isotope-labelled arginine through a colon catheter, using mass spectrometry. Isotope-labelled putrescine was detected in faecal cultures and colonic contents of rats injected with isotope-labelled arginine. Putrescine is produced through multiple pathways, and its extracellular intermediates are exchanged between bacterial species. Additionally, we demonstrated that the collective metabolic pathway depends on a complex exchange of metabolites released into the colonic lumen. This study demonstrates the existence of putrescine biosynthetic pathways based on the collective metabolic functions of the intestinal microbial community. Our findings provide knowledge to manipulate the levels of intestinal microbial products, including polyamines, that may modulate host health.
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Affiliation(s)
- Atsuo Nakamura
- Dairy Science and Technology Institute, Kyodo Milk Industry Co., Ltd., Tokyo, Japan
| | - Takushi Ooga
- Human Metabolome Technologies Inc., Yamagata, Japan
| | - Mitsuharu Matsumoto
- Dairy Science and Technology Institute, Kyodo Milk Industry Co., Ltd., Tokyo, Japan,CONTACT Mitsuharu Matsumoto Dairy Science and Technology Institute, Kyodo Milk Industry Co., Ltd., 20-1 Hirai, Hinode, Nishitama 190-0182, Tokyo, Japan
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37
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Majsnerowska M, Noens EEE, Lolkema JS. Arginine and Citrulline Catabolic Pathways Encoded by the arc Gene Cluster of Lactobacillus brevis ATCC 367. J Bacteriol 2018; 200:e00182-18. [PMID: 29712874 PMCID: PMC6018368 DOI: 10.1128/jb.00182-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/23/2018] [Indexed: 01/25/2023] Open
Abstract
High concentrations of l-arginine or l-citrulline in the growth medium provided the wine bacterium Lactobacillus brevis with a significant growth advantage. The arginine deiminase pathway (ADI) arc gene cluster of Lactobacillus brevis contains three genes-arcD, arcE1, and arcE2-encoding putative l-arginine/l-ornithine exchangers. Uptake experiments with Lactococcus lactis cells expressing the genes showed that all three transported l-ornithine with affinities in the micromolar range. Similarly, ArcD and ArcE2 transported l-arginine, while ArcE1 transported l-citrulline, an intermediate of the ADI pathway. Chase experiments showed very efficient exchange of l-arginine and l-ornithine by ArcD and ArcE2 and of l-citrulline and l-ornithine by ArcE1. Low affinities (millimolar range) combined with low translocation rates were found for ArcD and ArcE2 with l-citrulline and for ArcE1 with l-arginine. Resting cells of Lactobacillus brevis grown in the presence of l-arginine and l-citrulline rapidly consumed l-arginine and l-citrulline, respectively, while producing ammonia and l-ornithine. About 10% of l-arginine degraded was excreted by the cells as l-citrulline. Degradation of l-arginine and l-citrulline was not subject to carbon catabolite repression by glucose in the medium. At a high medium pH, l-citrulline in the medium was required for induction of the l-citrulline degradation pathway. Pathways are proposed for the catabolic breakdown of l-arginine and l-citrulline that merge at the level of ornithine transcarbamylase in the ADI pathway. l-Arginine uptake is catalyzed by ArcD and/or ArcE2, l-citrulline by ArcE1. l-Citrulline excretion during l-arginine breakdown is proposed to be catalyzed by ArcD and/or ArcE2 through l-arginine/l-citrulline exchange.IMPORTANCELactobacillus brevis, a bacterium isolated from wine, as well as other food environments, expresses a catabolic pathway for the breakdown of l-citrulline in the medium that consists of the l-citrulline/l-ornithine exchanger ArcE1 and part of the catabolic arginine deiminase (ADI) pathway enzymes. The proposed pathways for l-arginine and l-citrulline breakdown provide a mechanism for l-citrulline accumulation in fermented food products that is the precursor of the carcinogen ethyl carbamate.
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Affiliation(s)
- Maria Majsnerowska
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Elke E E Noens
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Juke S Lolkema
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Chen X, Ma A, McDermaid A, Zhang H, Liu C, Cao H, Ma Q. RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis. Genes (Basel) 2018; 9:genes9060278. [PMID: 29849014 PMCID: PMC6027394 DOI: 10.3390/genes9060278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/19/2018] [Accepted: 05/25/2018] [Indexed: 11/16/2022] Open
Abstract
Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to be connected with acid stress response. Validated by literature, 33 genes in Lactococcus lactis MG1363 were found to have orthologous genes which were associated with six regulons. An acid response related regulatory network was constructed, involving two trans-membrane proteins, eight regulons (llrA, llrC, hllA, ccpA, NHP6A, rcfB, regulons #8 and #39), nine functional modules, and 33 genes with orthologous genes known to be associated with acid stress. The predicted response pathways could serve as promising candidates for better acid tolerance engineering in Lactococcus lactis. Our RECTA pipeline provides an effective way to construct a reliable gene regulatory network through regulon elucidation, and has strong application power and can be effectively applied to other bacterial genomes where the elucidation of the transcriptional regulation network is needed.
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Affiliation(s)
- Xin Chen
- Center for Applied Mathematics, Tianjin University, Tianjin 300072, China.
| | - Anjun Ma
- Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57006, USA.
| | - Adam McDermaid
- Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57006, USA.
| | - Hanyuan Zhang
- College of Computer Science and Engineering, University of Nebraska Lincoln, Lincoln, NE 68588, USA.
| | - Chao Liu
- Shandong Provincial Hospital affiliated to Shandong University, Jinan 250021, China.
| | - Huansheng Cao
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Qin Ma
- Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57006, USA.
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Fraunhofer ME, Jakob F, Vogel RF. Influence of Different Sugars and Initial pH on β-Glucan Formation by Lactobacillus brevis TMW 1.2112. Curr Microbiol 2018; 75:794-802. [DOI: 10.1007/s00284-018-1450-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 02/05/2018] [Indexed: 11/29/2022]
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40
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The late blowing defect of hard cheeses: Behaviour of cells and spores of Clostridium tyrobutyricum throughout the cheese manufacturing and ripening. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.08.083] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Joshi V, Fernie AR. Citrulline metabolism in plants. Amino Acids 2017; 49:1543-1559. [PMID: 28741223 DOI: 10.1007/s00726-017-2468-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/17/2017] [Indexed: 11/28/2022]
Abstract
Citrulline was chemically isolated more than 100 years ago and is ubiquitous in animals, plants, bacteria, and fungi. Most of the research on plant citrulline metabolism and transport has been carried out in Arabidopsis thaliana and the Cucurbitaceae family, particularly in watermelon which accumulates this non-proteinogenic amino acid to very high levels. Industrially, citrulline is produced via specially optimized microbial strains; however, the amounts present in watermelon render it an economically viable source providing that other high-value compounds can be co-extracted. In this review, we provide an overview of our current understanding of citrulline biosynthesis, transport, and catabolism in plants additionally pointing out significant gaps in our knowledge which need to be closed by future experimentation. This includes the identification of further potential enzymes of citrulline metabolism as well as obtaining a far better spatial resolution of both sub-cellular and long-distance partitioning of citrulline. We further discuss what is known concerning the biological function of citrulline in plants paying particular attention to the proposed roles in scavenging of excess NH4+ and as a compatible solute.
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Affiliation(s)
- Vijay Joshi
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Uvalde, TX, 78801, USA.
| | - Alisdair R Fernie
- Max-Planck-Institute for Molecular Plant Physiology, Wissenschaftspark Golm, 14476, Potsdam-Golm, Germany
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Rozo ZLC, Márquez-Ortiz RA, Castro BE, Gómez NV, Escobar-Pérez J. Participation of the arcRACME protein in self-activation of the arc operon located in the arginine catabolism mobile element in pandemic clone USA300. Mem Inst Oswaldo Cruz 2017; 112:499-503. [PMID: 28591311 PMCID: PMC5452487 DOI: 10.1590/0074-02760160424] [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: 09/19/2016] [Accepted: 03/04/2017] [Indexed: 11/21/2022] Open
Abstract
Staphylococcus aureus pandemic clone USA300 has, in addition to its constitutive arginine catabolism (arc) gene cluster, an arginine catabolism mobile element (ACME) carrying another such cluster, which gives this clone advantages in colonisation and infection. Gene arcR, which encodes an oxygen-sensitive transcriptional regulator, is inside ACME and downstream of the constitutive arc gene cluster, and this situation may have an impact on its activation. Different relative expression behaviours are proven here for arcRACME and the arcACME operon compared to the constitutive ones. We also show that the artificially expressed recombinant ArcRACME protein binds to the promoter region of the arcACME operon; this mechanism can be related to a positive feedback model, which may be responsible for increased anaerobic survival of the USA300 clone during infection-related processes.
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43
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Golyshina OV, Tran H, Reva ON, Lemak S, Yakunin AF, Goesmann A, Nechitaylo TY, LaCono V, Smedile F, Slesarev A, Rojo D, Barbas C, Ferrer M, Yakimov MM, Golyshin PN. Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum Y T. Sci Rep 2017; 7:3682. [PMID: 28623373 PMCID: PMC5473848 DOI: 10.1038/s41598-017-03904-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/02/2017] [Indexed: 12/19/2022] Open
Abstract
Ferroplasmaceae represent ubiquitous iron-oxidising extreme acidophiles with a number of unique physiological traits. In a genome-based study of Ferroplasma acidiphilum YT, the only species of the genus Ferroplasma with a validly published name, we assessed its central metabolism and genome stability during a long-term cultivation experiment. Consistently with physiology, the genome analysis points to F. acidiphilum YT having an obligate peptidolytic oligotrophic lifestyle alongside with anaplerotic carbon assimilation. This narrow trophic specialisation abridges the sugar uptake, although all genes for glycolysis and gluconeogenesis, including bifunctional unidirectional fructose 1,6-bisphosphate aldolase/phosphatase, have been identified. Pyruvate and 2-oxoglutarate dehydrogenases are substituted by 'ancient' CoA-dependent pyruvate and alpha-ketoglutarate ferredoxin oxidoreductases. In the lab culture, after ~550 generations, the strain exhibited the mutation rate of ≥1.3 × 10-8 single nucleotide substitutions per site per generation, which is among the highest values recorded for unicellular organisms. All but one base substitutions were G:C to A:T, their distribution between coding and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the neutral drift being a prevalent mode in genome evolution in the lab culture. Mutations in nature seem to occur with lower frequencies, as suggested by a remarkable genomic conservation in F. acidiphilum YT variants from geographically distant populations.
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Affiliation(s)
- Olga V Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, Gwynedd, UK.
| | - Hai Tran
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, Gwynedd, UK
| | - Oleg N Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, 0002, South Africa
| | - Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S3E5, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S3E5, Toronto, Ontario, Canada
| | - Alexander Goesmann
- CeBiTec Bielefeld University, Universitätsstraße 25, D-33615, Bielefeld, Germany
- Department of Bioinformatics and Systems Biology, Justus Liebig Universität Gießen, Heinrich-Buff-Ring 58, D-35392, Gießen, Germany
| | - Taras Y Nechitaylo
- Insect Symbiosis Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Violetta LaCono
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Alexei Slesarev
- Fidelity Systems, Zylacta Corporation, 7965 Cessna Avenue, Gaithersburg, MD, 20879, USA
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Manuel Ferrer
- Institute of Catalysis CSIC, Campus Cantoblanco, 28049, Madrid, Spain
| | - Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
- Immanuel Kant Baltic Federal University, Universitetskaya 1, 36040, Kaliningrad, Russia
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, Gwynedd, UK
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Noens EEE, Lolkema JS. Convergent evolution of the arginine deiminase pathway: the ArcD and ArcE arginine/ornithine exchangers. Microbiologyopen 2017; 6:e00412. [PMID: 27804281 PMCID: PMC5300872 DOI: 10.1002/mbo3.412] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/30/2016] [Accepted: 09/01/2016] [Indexed: 11/10/2022] Open
Abstract
The arginine deiminase (ADI) pathway converts L-arginine into L-ornithine and yields 1 mol of ATP per mol of L-arginine consumed. The L-arginine/L-ornithine exchanger in the pathway takes up L-arginine and excretes L-ornithine from the cytoplasm. Analysis of the genomes of 1281 bacterial species revealed the presence of 124 arc gene clusters encoding the pathway. About half of the clusters contained the gene encoding the well-studied L-arginine/L-ornithine exchanger ArcD, while the other half contained a gene, termed here arcE, encoding a membrane protein that is not a homolog of ArcD. The arcE gene product of Streptococcus pneumoniae was shown to take up L-arginine and L-ornithine with affinities of 0.6 and 1 μmol/L, respectively, and to catalyze metabolic energy-independent, electroneutral exchange. ArcE of S. pneumoniae could replace ArcD in the ADI pathway of Lactococcus lactis and provided the cells with a growth advantage. In contrast to ArcD, ArcE catalyzed translocation of the pathway intermediate L-citrulline with high efficiency. A short version of the ADI pathway is proposed for L-citrulline catabolism and the presence of the evolutionary unrelated arcD and arcE genes in different organisms is discussed in the context of the evolution of the ADI pathway.
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Affiliation(s)
- Elke E. E. Noens
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Juke S. Lolkema
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
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Xiong L, Yang Y, Ye YN, Teng JLL, Chan E, Watt RM, Guo FB, Lau SKP, Woo PCY. Laribacter hongkongensis anaerobic adaptation mediated by arginine metabolism is controlled by the cooperation of FNR and ArgR. Environ Microbiol 2017; 19:1266-1280. [PMID: 28028888 DOI: 10.1111/1462-2920.13657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/19/2016] [Accepted: 12/21/2016] [Indexed: 11/27/2022]
Abstract
Laribacter hongkongensis is a fish-borne pathogen associated with invasive infections and gastroenteritis. Its adaptive mechanisms to oxygen-limiting conditions in various environmental niches remain unclear. In this study, we compared the transcriptional profiles of L. hongkongensis under aerobic and anaerobic conditions using RNA-sequencing. Expression of genes involved in arginine metabolism significantly increased under anoxic conditions. Arginine was exploited as the sole energy source in L. hongkongensis for anaerobic respiration via the arginine catabolism pathway: specifically via the arginine deiminase (ADI) pathway. A transcriptional regulator FNR was identified to coordinate anaerobic metabolism by tightly regulating the expression of arginine metabolism genes. FNR executed its regulatory function by binding to FNR boxes in arc operons promoters. Survival of isogenic fnr mutant in macrophages decreased significantly when compared with wild-type; and expression level of fnr increased 8 h post-infection. Remarkably, FNR directly interacted with ArgR, another regulator that influences the biological fitness and intracellular survival of L. hongkongensis by regulating arginine metabolism genes. Our results demonstrated that FNR and ArgR work in coordination to respond to oxygen changes in both extracellular and intracellular environments, by finely regulating the ADI pathway and arginine anabolism pathways, thereby optimizing bacterial fitness in various environmental niches.
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Affiliation(s)
- Lifeng Xiong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.,Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Ying Yang
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Yuan-Nong Ye
- School of Biology and Engineering, Guizhou Medical University, Guizhou, China
| | - Jade L L Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
| | - Elaine Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Rory M Watt
- Applied Oral Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong
| | - Feng-Biao Guo
- Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Patrick C Y Woo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.,Department of Microbiology, The University of Hong Kong, Hong Kong.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
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Novák L, Zubáčová Z, Karnkowska A, Kolisko M, Hroudová M, Stairs CW, Simpson AGB, Keeling PJ, Roger AJ, Čepička I, Hampl V. Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes. BMC Evol Biol 2016; 16:197. [PMID: 27716026 PMCID: PMC5052871 DOI: 10.1186/s12862-016-0771-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 09/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. RESULTS We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. CONCLUSIONS Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.
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Affiliation(s)
- Lukáš Novák
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Zuzana Zubáčová
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Anna Karnkowska
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Martin Kolisko
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Miluše Hroudová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Courtney W. Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | | | | | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Ivan Čepička
- Department of Zoology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
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FlpS, the FNR-Like Protein of Streptococcus suis Is an Essential, Oxygen-Sensing Activator of the Arginine Deiminase System. Pathogens 2016; 5:pathogens5030051. [PMID: 27455333 PMCID: PMC5039431 DOI: 10.3390/pathogens5030051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/07/2016] [Accepted: 07/14/2016] [Indexed: 11/17/2022] Open
Abstract
Streptococcus (S.) suis is a zoonotic pathogen causing septicemia and meningitis in pigs and humans. During infection S. suis must metabolically adapt to extremely diverse environments of the host. CcpA and the FNR family of bacterial transcriptional regulators are important for metabolic gene regulation in various bacteria. The role of CcpA in S. suis is well defined, but the function of the FNR-like protein of S. suis, FlpS, is yet unknown. Transcriptome analyses of wild-type S. suis and a flpS mutant strain suggested that FlpS is involved in the regulation of the central carbon, arginine degradation and nucleotide metabolism. However, isotopologue profiling revealed no substantial changes in the core carbon and amino acid de novo biosynthesis. FlpS was essential for the induction of the arcABC operon of the arginine degrading pathway under aerobic and anaerobic conditions. The arcABC-inducing activity of FlpS could be associated with the level of free oxygen in the culture medium. FlpS was necessary for arcABC-dependent intracellular bacterial survival but redundant in a mice infection model. Based on these results, we propose that the core function of S. suis FlpS is the oxygen-dependent activation of the arginine deiminase system.
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Phenotype microarray analysis may unravel genetic determinants of the stress response by Rhodococcus aetherivorans BCP1 and Rhodococcus opacus R7. Res Microbiol 2016; 167:766-773. [PMID: 27394988 DOI: 10.1016/j.resmic.2016.06.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/24/2016] [Accepted: 06/24/2016] [Indexed: 11/23/2022]
Abstract
In the present study, the response of Rhodococcus aetherivorans BCP1 and Rhodococcus opacus R7 to various stress conditions and several antimicrobials was examined by PM in relation with genetic determinants, as revealed by annotation analysis of the two genomes. Comparison between metabolic activities and genetic features of BCP1 and R7 provided new insight into the environmental persistence of these two members of the genus Rhodococcus.
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49
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Deng P, Wang X, Baird SM, Showmaker KC, Smith L, Peterson DG, Lu S. Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis. Microbiologyopen 2016; 5:353-69. [PMID: 26769582 PMCID: PMC4905989 DOI: 10.1002/mbo3.333] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/22/2015] [Accepted: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
Burkholderia contaminans MS14 shows significant antimicrobial activities against plant and animal pathogenic fungi and bacteria. The antifungal agent occidiofungin produced by MS14 has great potential for development of biopesticides and pharmaceutical drugs. However, the use of Burkholderia species as biocontrol agent in agriculture is restricted due to the difficulties in distinguishing between plant growth-promoting bacteria and the pathogenic bacteria. The complete MS14 genome was sequenced and analyzed to find what beneficial and virulence-related genes it harbors. The phylogenetic relatedness of B. contaminans MS14 and other 17 Burkholderia species was also analyzed. To research MS14's potential virulence, the gene regions related to the antibiotic production, antibiotic resistance, and virulence were compared between MS14 and other Burkholderia genomes. The genome of B. contaminans MS14 was sequenced and annotated. The genomic analyses reveal the presence of multiple gene sets for antimicrobial biosynthesis, which contribute to its antimicrobial activities. BLAST results indicate that the MS14 genome harbors a large number of unique regions. MS14 is closely related to another plant growth-promoting Burkholderia strain B. lata 383 according to the average nucleotide identity data. Moreover, according to the phylogenetic analysis, plant growth-promoting species isolated from soils and mammalian pathogenic species are clustered together, respectively. MS14 has multiple antimicrobial activity-related genes identified from the genome, but it lacks key virulence-related gene loci found in the pathogenic strains. Additionally, plant growth-promoting Burkholderia species have one or more antimicrobial biosynthesis genes in their genomes as compared with nonplant growth-promoting soil-isolated Burkholderia species. On the other hand, pathogenic species harbor multiple virulence-associated gene loci that are not present in nonpathogenic Burkholderia species. The MS14 genome as well as Burkholderia species genome show considerable diversity. Multiple antimicrobial agent biosynthesis genes were identified in the genome of plant growth-promoting species of Burkholderia. In addition, by comparing to nonpathogenic Burkholderia species, pathogenic Burkholderia species have more characterized homologs of the gene loci known to contribute to pathogenicity and virulence to plant and animals.
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Affiliation(s)
- Peng Deng
- Departments of Biochemistry, Molecular BiologyEntomology and Plant PathologyMississippi State UniversityMississippi stateMississippi
| | - Xiaoqiang Wang
- Departments of Biochemistry, Molecular BiologyEntomology and Plant PathologyMississippi State UniversityMississippi stateMississippi
| | - Sonya M. Baird
- Departments of Biochemistry, Molecular BiologyEntomology and Plant PathologyMississippi State UniversityMississippi stateMississippi
| | - Kurt C. Showmaker
- Institute for GenomicsBiocomputing and BiotechnologyMississippi State UniversityMississippi stateMississippi
| | - Leif Smith
- Department of BiologyTexas A&M UniversityCollege StationTexas
| | - Daniel G. Peterson
- Institute for GenomicsBiocomputing and BiotechnologyMississippi State UniversityMississippi stateMississippi
| | - Shien Lu
- Departments of Biochemistry, Molecular BiologyEntomology and Plant PathologyMississippi State UniversityMississippi stateMississippi
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Han RZ, Xu GC, Dong JJ, Ni Y. Arginine deiminase: recent advances in discovery, crystal structure, and protein engineering for improved properties as an anti-tumor drug. Appl Microbiol Biotechnol 2016; 100:4747-60. [DOI: 10.1007/s00253-016-7490-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 02/06/2023]
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