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Mohammadi M, Attar A, Mohammadbeigi M, Peymani A, Bolori S, Fardsanei F. The possible role of Helicobacter pylori in liver diseases. Arch Microbiol 2023; 205:281. [PMID: 37430019 DOI: 10.1007/s00203-023-03602-z] [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: 02/27/2023] [Revised: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 07/12/2023]
Abstract
According to previous studies, Helicobacter pylori infection is associated with liver disease. In order to better understand the risk of acquiring various liver diseases, we reviewed current knowledge on the impact of H. pylori on the onset, intensification, and progression of various liver diseases caused by the infection of H. pylori. It has been estimated that between 50 and 90% of people worldwide have been infected with H. pylori. The bacterium is mostly responsible for inflamed gastric mucosa, ulcers, and cancers associated with the gastric mucosa. Through the active antioxidant system in H. pylori, the bacteria can neutralize free radicals by synthesizing VacA, a toxin that causes cell damage and apoptosis. Furthermore, there is a possibility that CagA genes may play a role in cancer development. People who have been infected with H. pylori are likely to develop lesions in the skin, the circulation system, and the pancreas. Moreover, transferring blood from the stomach may allow H. pylori to colonize the liver. The bacterium worsened liver function during autoimmune inflammation, toxic injury, chronic HCV infection, chronic HBV infection, and liver cirrhosis. Increasing portal pressure, hyperammonemia, and esophageal varices may be associated with H pylori infection. As a result, it is crucial to diagnose and treat this infection in patients with H. pylori.
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Affiliation(s)
- Mahnaz Mohammadi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Adeleh Attar
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Maryam Mohammadbeigi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amir Peymani
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Shahin Bolori
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Fatemeh Fardsanei
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran.
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Mordhorst S, Badmann T, Bösch NM, Morinaka BI, Rauch H, Piel J, Groll M, Vagstad AL. Structural and Biochemical Insights into Post-Translational Arginine-to-Ornithine Peptide Modifications by an Atypical Arginase. ACS Chem Biol 2023; 18:528-536. [PMID: 36791048 PMCID: PMC10028609 DOI: 10.1021/acschembio.2c00879] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Landornamide A is a ribosomally synthesized and post-translationally modified peptide (RiPP) natural product with antiviral activity. Its biosynthetic gene cluster encodes─among other maturases─the peptide arginase OspR, which converts arginine to ornithine units in an unusual post-translational modification. Peptide arginases are a recently discovered RiPP maturase family with few characterized representatives. They show little sequence similarity to conventional arginases, a well-characterized enzyme family catalyzing the hydrolysis of free arginine to ornithine and urea. Peptide arginases are highly promiscuous and accept a variety of substrate sequences. The molecular basis for binding the large peptide substrate and for the high promiscuity of peptide arginases remains unclear. Here, we report the first crystal structure of a peptide arginase at a resolution of 2.6 Å. The three-dimensional structure reveals common features and differences between conventional arginases and the peptide arginase: the binuclear metal cluster and the active-site environment strongly resemble each other, while the quaternary structures diverge. Kinetic analyses of OspR with various substrates provide new insights into the order of biosynthetic reactions during the post-translational maturation of landornamide A. These results provide the basis for pathway engineering to generate derivatives of landornamide A and for the general application of peptide arginases as biosynthetic tools for peptide engineering.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Thomas Badmann
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Nina M Bösch
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Brandon I Morinaka
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Hartmut Rauch
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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Ethica SN, Zilda DS, Oedjijono O, Muhtadi M, Patantis G, Darmawati S, Dewi SS, Sabdono A, Uria AR. Biotechnologically potential genes in a polysaccharide-degrading epibiont of the Indonesian brown algae Hydroclathrus sp. J Genet Eng Biotechnol 2023; 21:18. [PMID: 36786886 PMCID: PMC9928984 DOI: 10.1186/s43141-023-00461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/06/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND Marine bacteria have recently attracted increasing attention to be harnessed for the production of valuable enzymes, vitamins, and bioactive compounds. Bacteria associated with the surfaces of marine macroalgae, called epibionts, are particularly interesting from ecological and biotechnological points of view, as they often exhibit antimicrobial activities to compete with pathogenic bacteria for nutrients and spaces. In search for biotechnologically potential genes from marine bacteria, we sequenced and analysed the genome of the epibiont HI03-3b, a polysaccharide-degrading bacterium associated with the surface of the Indonesian brown algae Hydroclathrus sp. RESULTS The algal epibiont HI03-3b has a genome of approximately 4,860,704 bp in size with 42.02 mol% G + C content, consisting of 5655 open reading frames (ORFs), 4409 genes coding for proteins (CDSs), 94 genes for tRNAs, and 32 genes for rRNAs. The genome sequence of HI03-3b was most closely related to that of Cytobacillus firmus NCTC10335 with the average amino acid identity (AAI) of 95.0 %, average nucleotide identity (ANI) of 94.1 %, and a recommended DNA-DNA hybridization (DDH) of 57.60 %. These scores are lower than the most frequently used standard for species demarcation (95% ANI cutoff) and the new species threshold (DDH > 70.0% for the same bacterial species). Some differences in genome features and gene composition were observed between HI03-3b and NCTC10335, such as genes encoding carbohydrate active enzymes. These suggest that HI03-3b is unique and likely a novel species within Cytobacillus genus, and we therefore proposed its name as Cytobacillus wakatobiense HI03-3b. Genome sequence analyses indicated the presence of genes involved not only in polysaccharide and protein degradation but also in vitamin and secondary metabolite biosynthesis. Some of them encode enzymes and compounds with biotechnological interest, such as protease, chitinase, subtilisin, pullulanase, and bacillolysin, which are often associated with antimicrobial or antibiofilm activities. This antimicrobial potential is supported by our finding that the extracellular protein fraction of this epibiont inhibited the growth of the bacterial pathogen Staphylococcus aureus. CONCLUSION The epibiont Cytobacillus HI03-3b harbours genes for polysaccharide and protein degradation as well as for natural product biosynthesis, suggesting its potential ecological roles in outcompeting other bacteria during biofilm formation as well as in protecting its algal host from predation. Due to the presence of genes for vitamin biosynthesis, it might also provide the algal host with vitamins for growth and development. Some of these metabolic genes are biotechnologically important, as they could become a platform for bioengineering to generate various seaweed-derived substances sustainably, such as antibiofilm agents and vitamins, which are beneficial for human health.
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Affiliation(s)
- Stalis Norma Ethica
- grid.444265.50000 0004 0386 6520Magister Program of Clinical Laboratory Science, Universitas Muhammadiyah Semarang (UNIMUS), Jalan Kedungmundu Raya, Semarang, 50273 Indonesia
| | - Dewi Seswita Zilda
- Research Center for Deep Sea, Earth Sciences and Maritime Research Organization, National Research and Innovation Agency (BRIN), Jl. Pasir Putih Raya, Pademangan, North Jakarta City, Jakarta 14430 Indonesia
| | - Oedjijono Oedjijono
- grid.444191.d0000 0000 9134 0078Faculty of Biology, Universitas Jenderal Soedirman, Purwokerto, 53122 Indonesia
| | - Muhtadi Muhtadi
- grid.444490.90000 0000 8731 0765Faculty of Pharmacy, Universitas Muhammadiyah Surakarta (UMS), Sukoharjo, 57162 Indonesia
| | - Gintung Patantis
- Research Center for Marine and Land Bioindustry, Earth Sciences and Maritime Research Organization, National Research and Innovation Agency (BRIN), Kodek Bay, North Lombok, West Nusa Tenggara 83352 Indonesia
| | - Sri Darmawati
- grid.444265.50000 0004 0386 6520Magister Program of Clinical Laboratory Science, Universitas Muhammadiyah Semarang (UNIMUS), Jalan Kedungmundu Raya, Semarang, 50273 Indonesia
| | - Sri Sinto Dewi
- grid.444265.50000 0004 0386 6520Diploma Study Program of Medical Laboratory Technology, Faculty of Nursing and Health Sciences, Universitas Muhammadiyah Semarang, Semarang, 50273 Indonesia
| | - Agus Sabdono
- grid.412032.60000 0001 0744 0787Department of Marine Science, Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, 50272 Indonesia
| | - Agustinus Robert Uria
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12 Nishi 6 Kita-ku, Sapporo, 060-0812, Japan. .,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita 12 Nishi 6, Sapporo, 060-0812, Japan.
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Role and Application of Biocatalysts in Cancer Drug Discovery. Catalysts 2023. [DOI: 10.3390/catal13020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A biocatalyst is an enzyme that speeds up or slows down the rate at which a chemical reaction occurs and speeds up certain processes by 108 times. It is used as an anticancer agent because it targets drug activation inside the tumor microenvironment while limiting damage to healthy cells. Biocatalysts have been used for the synthesis of different heterocyclic compounds and is also used in the nano drug delivery systems. The use of nano-biocatalysts for tumor-targeted delivery not only aids in tumor invasion, angiogenesis, and mutagenesis, but also provides information on the expression and activity of many markers related to the microenvironment. Iosmapinol, moclobemide, cinepazide, lysine dioxygenase, epothilone, 1-homophenylalanine, and many more are only some of the anticancer medicines that have been synthesised using biocatalysts. In this review, we have highlighted the application of biocatalysts in cancer therapies as well as the use of biocatalysts in the synthesis of drugs and drug-delivery systems in the tumor microenvironment.
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Patel D, Lee TJ, Kumar S, Vyavahare S, Worth A, Hill WD, Hamrick M, Isales CM, Shinde RS, Fulzele S. Alterations in bone metabolites with age in C57BL/6 mice model. Biogerontology 2022; 23:629-640. [PMID: 36056226 PMCID: PMC10918568 DOI: 10.1007/s10522-022-09986-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/17/2022] [Indexed: 11/28/2022]
Abstract
Understanding the pathophysiology behind age-related diseases is an urgent need as the elderly population continues to grow. With age, there is a high risk of musculoskeletal deterioration and associated morbidity and mortality. Although the exact mechanism behind age-related degeneration is unknown, it is well established that alteration in cellular metabolism is one of the important contributing factors. Alteration in signaling pathways with age leads to the accumulation or depletion of several metabolites that play a vital role in musculoskeletal pathophysiology. This study aimed to identify age-related changes in bone tissue metabolites in C57BL/6 mice. We then correlated the differentially expressed metabolites with their functions in bone biology. In both aged males and females, hydroxyproline, glutamine, and alpha-linolenic acid levels were decreased. In aged females, Ornithine (p value = 0.001), L-Proline (p value = 0.008), Uridine (p value = 0.001), Aspartic Acid (p value = 0.004) levels were significantly decreased, and glutamate (p value = 0.002) was elevated. In aged males, N-acetyl-D-glucosamine (pvalue = 0.010), Adrenic acid (pvalue = 0.0099), Arachidonic acid (p value = 0.029) and Allantoin (p value = 0.004) levels were decreased. Metabolic pathway analysis revealed that purine and D-glutamine and D-glutamate metabolism were significantly altered in both sexes, while arginine biosynthesis in females and lipid metabolism in males were highly affected. These differences in metabolic signaling might be one of the reasons for the discrepancy in musculoskeletal disease manifestation between the two sexes. Understanding the role of these metabolites play in the aging bone will allow for new sex-specific targeted therapies against the progression of musculoskeletal diseases.
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Affiliation(s)
- Dhara Patel
- Department of Medicine, Augusta University, Augusta, GA, 30912, USA
| | - Tae Jin Lee
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA, 30912, USA
| | - Sandeep Kumar
- Department of Cell Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - Sagar Vyavahare
- Department of Cell Biology and Anatomy, Augusta University, Augusta, GA, USA
| | - Alison Worth
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute Cancer Center, Philadelphia, PA, USA
| | - William D Hill
- Medical University of South Carolina, Charleston, SC, 29403, USA
| | - Mark Hamrick
- Department of Cell Biology and Anatomy, Augusta University, Augusta, GA, USA
- Center for Healthy Aging, Augusta University, Augusta, GA, USA
| | - Carlos M Isales
- Department of Medicine, Augusta University, Augusta, GA, 30912, USA
- Center for Healthy Aging, Augusta University, Augusta, GA, USA
| | - Rahul S Shinde
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute Cancer Center, Philadelphia, PA, USA
| | - Sadanand Fulzele
- Department of Medicine, Augusta University, Augusta, GA, 30912, USA.
- Department of Cell Biology and Anatomy, Augusta University, Augusta, GA, USA.
- Center for Healthy Aging, Augusta University, Augusta, GA, USA.
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K D, Kuramitsu S, Yokoyama S, Thirumananseri K, Ponnuraj K. Crystal structure analysis and molecular dynamics simulations of arginase from Thermus thermophilus. J Biomol Struct Dyn 2022:1-11. [PMID: 35994323 DOI: 10.1080/07391102.2022.2112615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Arginase is a manganese-dependent metalloenzyme that catalyzes the hydrolysis of L-arginine to L-ornithine and urea. The product L-ornithine is an important component which has wide applications in the healthcare and pharmaceutical industry. Enzymatic biosynthesis of L-ornithine is one of the effective methods in which arginase is used as a bio-catalyst. Here, we report the crystal structure of arginase from Thermus thermophilus (TtArginase) in three different crystal forms. All structures were solved by molecular replacement and refined at 2.0 Å, 2.3 Å and 2.91 Å resolution respectively. TtArginase is compared with other structural homologs and the putative catalytic site residues were identified. To understand the thermophilic nature of TtArginase, the sequence and structural factors of TtArginase was compared with its mesophilic counterpart Bacillus subtilis arginase (BsArginase). To get insights on structural stability, molecular dynamics (MD) simulations were carried for TtArginase and BsArginase at three different temperatures (300 K, 333 K and 353 K). The results indicate that TtArginase is comparatively more stable than BsArginase. MD simulations were carried out in the absence of the metal ions at the active site which revealed high plasticity of the active site. The results suggest that metal ions are critical not only for the catalytic function, but also required for the maintenance of the proper active site geometry. Since arginase can be employed for large-scale industrial production of L-ornithine, the structural details of thermophilic arginases such as TtArginase will be helpful to engineer the protein to optimize its enzymatic action in a variety of conditions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhanalakshmi K
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
| | - Seiki Kuramitsu
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Shigeyuki Yokoyama
- Structural Biology Laboratory, RIKEN Yokohama Institute, RIKEN, Tsurumi, Yokohama, Japan
| | - Kumarevel Thirumananseri
- Structural Biology Laboratory, RIKEN Yokohama Institute, RIKEN, Tsurumi, Yokohama, Japan.,Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamic Research, RIKEN Yokohama Institute, Tsurumi, Yokohama, Japan
| | - Karthe Ponnuraj
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
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