1
|
Khamis AA, Sharshar AH, Mohamed TM, Abdelrasoul EA, Salem MM. Visnagin alleviates rheumatoid arthritis via its potential inhibitory impact on malate dehydrogenase enzyme: in silico, in vitro, and in vivo studies. GENES & NUTRITION 2024; 19:20. [PMID: 39390383 PMCID: PMC11465529 DOI: 10.1186/s12263-024-00756-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 09/13/2024] [Indexed: 10/12/2024]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disorder. The present study aimed to evaluate the in silico, in vitro, and in vivo inhibitory effect of visnagin on malate dehydrogenase activity and elucidate its inflammatory efficacy when combined with methotrexate in the RA rat model. The molecular docking, ADMET simulations, MDH activity, expression, and X-ray imaging were detected. Moreover, CRP, RF, (anti-CCP) antibody, (TNF-α), (IL-6), (IL-17), and (IL-10) were evaluated. The expression levels of MMP3 and FOXP3 genes and CD4, CD25, and CD127 protein levels were assessed. Histological assessment of ankle joints was evaluated. The results revealed that visnagin showed reversible competitive inhibition on MDH with inhibitory constant (Ki) equal to 141 mM with theoretical IC50 equal to 1202.7 mM, LD50 equal to 155.39 mg/kg, and LD25 equal to 77.69 mg/kg. In vivo studies indicated that visnagin exhibited anti-inflammatory effects through decreasing MDH1 activity and expression and induced proliferation of anti-inflammatory CD4+CD25+FOXP3 regulatory T cells with increasing the anti-inflammatory cytokine IL-10 levels. Moreover, visnagin reduced the levels of inflammatory cytokines and the immuno-markers. Our findings elucidate that visnagin exhibits an anti-inflammatory impact against RA through its ability to inhibit the MDH1 enzyme, improve methotrexate efficacy, and reduce oxidative stress.
Collapse
Affiliation(s)
- Abeer A Khamis
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, Egypt.
| | - Amira H Sharshar
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Tarek M Mohamed
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Elsayed A Abdelrasoul
- Head Researcher of Special Food and Nutrition Department, Food Technology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Maha M Salem
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, Egypt
| |
Collapse
|
2
|
Wang K, Shu C, Bravo A, Soberón M, Zhang H, Crickmore N, Zhang J. Development of an Online Genome Sequence Comparison Resource for Bacillus cereus sensu lato Strains Using the Efficient Composition Vector Method. Toxins (Basel) 2023; 15:393. [PMID: 37368694 DOI: 10.3390/toxins15060393] [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: 03/23/2023] [Revised: 05/21/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
An automated method was developed for differentiating closely related B. cereus sensu lato (s.l.) species, especially biopesticide Bacillus thuringiensis, from other human pathogens, B. anthracis and B. cereus sensu stricto (s.s.). In the current research, four typing methods were initially compared, including multi-locus sequence typing (MLST), single-copy core genes phylogenetic analysis (SCCGPA), dispensable genes content pattern analysis (DGCPA) and composition vector tree (CVTree), to analyze the genomic variability of 23 B. thuringiensis strains from aizawai, kurstaki, israelensis, thuringiensis and morrisoni serovars. The CVTree method was the best option to be used for typing B. thuringiensis strains since it proved to be the fastest method, whilst giving high-resolution data about the strains. In addition, CVTree agrees well with ANI-based method, revealing the relationship between B. thuringiensis and other B. cereus s.l. species. Based on these data, an online genome sequence comparison resource was built for Bacillus strains called the Bacillus Typing Bioinformatics Database to facilitate strain identification and characterization.
Collapse
Affiliation(s)
- Kui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Changlong Shu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Alejandra Bravo
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62250, Mexico
| | - Mario Soberón
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62250, Mexico
| | - Hongjun Zhang
- Institute for the Control of Agrochemicals, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Neil Crickmore
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| |
Collapse
|
3
|
El-Said KS, Atta A, Mobasher MA, Germoush MO, Mohamed TM, Salem MM. Quercetin mitigates rheumatoid arthritis by inhibiting adenosine deaminase in rats. Mol Med 2022; 28:24. [PMID: 35193490 PMCID: PMC8862293 DOI: 10.1186/s10020-022-00432-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/03/2022] [Indexed: 01/01/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory joint disease characterized by synovial proliferation and bone destruction. Adenosine deaminase (ADA) is a key inflammatory enzyme that increases joint stiffness and pain in RA. In this study, we evaluated the in-silico, and in vivo inhibitory effect of quercetin isolated from Egyptian Fenugreek on ADA enzyme activity. We also determined the combinatorial effect of quercetin on methotrexate mediated anti-inflammatory efficacy and toxicity. In-silico molecular docking was conducted and confirmed in an in vivo RA rat model. The results showed that the inhibition constant of quercetin on joint ADA by docking and in-vitro was 61.9 and 55.5 mM, respectively. Therefore, quercetin exhibits anti-inflammatory effect in a rat RA model as evidenced by reducing the specific activity of ADA in joint tissues, lower jaw volume, enhance body weight, downregulate ADA gene expression, reduce levels of RA cytokines interleukin-1β, interleukin-6, tumor necrosis factor-α, also, rheumatoid factor, C-reactive protein, and anti-cyclic citrullinated peptide RA biomarker levels. These findings demonstrate that the purified quercetin has a promising anti-inflammatory effect against RA disease through its inhibitory effects on the ADA enzyme. Furthermore, isolated quercetin improved the anti-inflammatory efficacy of methotrexate, reduced its toxic effects by increasing antioxidant enzymes and reducing oxidative stress.
Collapse
Affiliation(s)
- Karim Samy El-Said
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Amira Atta
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Maysa A Mobasher
- Pathology Department, Biochemistry Division, College of Medicine, Jouf University, Sakaka, 41412, Saudi Arabia
| | - Mousa O Germoush
- Biology Department, College of Science, Jouf University, Sakaka, 41412, Saudi Arabia
| | - Tarek M Mohamed
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Maha M Salem
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| |
Collapse
|
4
|
CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool based on Composition Vectors of Genomes. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:662-667. [PMID: 34119695 PMCID: PMC9040009 DOI: 10.1016/j.gpb.2021.03.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 02/23/2021] [Accepted: 03/06/2021] [Indexed: 11/21/2022]
Abstract
CVTree is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It had been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and fungi based on the whole genomes, as well as chloroplasts, mitochondria, and metagenomes. Here we presented the standalone software for the CVTree algorithm. In the software, an extensible parallel workflow for the CVTree algorithm was designed. Based on the workflow, new alignment-free methods were also implemented. And by examining the phylogeny and taxonomy of 13,903 prokaryotes based on 16S rRNA sequences, we showed that CVTree software is an efficient and effective tool for the studying of phylogeny and taxonomy based on genome sequences. Code availability: https://github.com/ghzuo/cvtree.
Collapse
|
5
|
Bünger W, Jiang X, Müller J, Hurek T, Reinhold-Hurek B. Novel cultivated endophytic Verrucomicrobia reveal deep-rooting traits of bacteria to associate with plants. Sci Rep 2020; 10:8692. [PMID: 32457320 PMCID: PMC7251102 DOI: 10.1038/s41598-020-65277-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/30/2020] [Indexed: 02/01/2023] Open
Abstract
Despite the relevance of complex root microbial communities for plant health, growth and productivity, the molecular basis of these plant-microbe interactions is not well understood. Verrucomicrobia are cosmopolitans in the rhizosphere, nevertheless their adaptations and functions are enigmatic since the proportion of cultured members is low. Here we report four cultivated Verrucomicrobia isolated from rice, putatively representing four novel species, and a novel subdivision. The aerobic strains were isolated from roots or rhizomes of Oryza sativa and O. longistaminata. Two of them are the first cultivated endophytes of Verrucomicrobia, as validated by confocal laser scanning microscopy inside rice roots after re-infection under sterile conditions. This extended known verrucomicrobial niche spaces. Two strains were promoting root growth of rice. Discovery of root compartment-specific Verrucomicrobia permitted an across-phylum comparison of the genomic conformance to life in soil, rhizoplane or inside roots. Genome-wide protein domain comparison with niche-specific reference bacteria from distant phyla revealed signature protein domains which differentiated lifestyles in these microhabitats. Our study enabled us to shed light into the dark microbial matter of root Verrucomicrobia, to define genetic drivers for niche adaptation of bacteria to plant roots, and provides cultured strains for revealing causal relationships in plant-microbe interactions by reductionist approaches.
Collapse
Affiliation(s)
- Wiebke Bünger
- Department of Microbe-Plant Interactions, University of Bremen, Bremen, Germany
| | - Xun Jiang
- Department of Microbe-Plant Interactions, University of Bremen, Bremen, Germany
| | - Jana Müller
- Department of Microbe-Plant Interactions, University of Bremen, Bremen, Germany.,Department of Botany, University of Bremen, Bremen, Germany
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, University of Bremen, Bremen, Germany
| | | |
Collapse
|
6
|
Li W, Freudenberg J, Freudenberg J. Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome. Gene 2019; 691:141-152. [PMID: 30630097 DOI: 10.1016/j.gene.2018.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/14/2018] [Indexed: 10/27/2022]
Abstract
The nuclear human genome harbors sequences of mitochondrial origin, indicating an ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments (NUMTs) have been detected by alignment-based sequence similarity search, as implemented in the Basic Local Alignment Search Tool (BLAST). Identifying NUMTs is important for the comprehensive annotation and understanding of the human genome. Here we explore the possibility of detecting NUMTs in the human genome by alignment-free sequence similarity search, such as k-mers (k-tuples, k-grams, oligos of length k) distributions. We find that when k=6 or larger, the k-mer approach and BLAST search produce almost identical results, e.g., detect the same set of NUMTs longer than 3 kb. However, when k=5 or k=4, certain signals are only detected by the alignment-free approach, and these may indicate yet unrecognized, and potentially more ancestral NUMTs. We introduce a "Manhattan plot" style representation of NUMT predictions across the genome, which are calculated based on the reciprocal of the Jensen-Shannon divergence between the nuclear and mitochondrial k-mer frequencies. The further inspection of the k-mer-based NUMT predictions however shows that most of them contain long-terminal-repeat (LTR) annotations, whereas BLAST-based NUMT predictions do not. Thus, similarity of the mitogenome to LTR sequences is recognized, which we validate by finding the mitochondrial k-mer distribution closer to those for transposable sequences and specifically, close to some types of LTR.
Collapse
Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.
| | - Jerome Freudenberg
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Jan Freudenberg
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| |
Collapse
|
7
|
On monospecific genera in prokaryotic taxonomy. Synth Syst Biotechnol 2018; 2:226-235. [PMID: 29318203 PMCID: PMC5655349 DOI: 10.1016/j.synbio.2017.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 11/24/2022] Open
Abstract
A monospecific genus contains a single species ever since it was proposed. Though formally more than half of the known prokaryotic genera are monospecific, we pick up those which actually raise taxonomic problems by violating monophyly of the taxon within which it resides. Taking monophyly as a guiding principle, our arguments are based on simultaneous support from 16S rRNA sequence analysis and whole-genome phylogeny of prokaryotes, as provided by the LVTree Viewer and CVTree Web Server, respectively. The main purpose of this study consists in calling attention to this specific way of global taxonomic analysis. Therefore, we refrain from making formal emendations for the time being.
Collapse
|
8
|
Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species. Proc Natl Acad Sci U S A 2018; 115:E753-E761. [PMID: 29317534 DOI: 10.1073/pnas.1715954115] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fungal genus of Aspergillus is highly interesting, containing everything from industrial cell factories, model organisms, and human pathogens. In particular, this group has a prolific production of bioactive secondary metabolites (SMs). In this work, four diverse Aspergillus species (A. campestris, A. novofumigatus, A. ochraceoroseus, and A. steynii) have been whole-genome PacBio sequenced to provide genetic references in three Aspergillus sections. A. taichungensis and A. candidus also were sequenced for SM elucidation. Thirteen Aspergillus genomes were analyzed with comparative genomics to determine phylogeny and genetic diversity, showing that each presented genome contains 15-27% genes not found in other sequenced Aspergilli. In particular, A. novofumigatus was compared with the pathogenic species A. fumigatus This suggests that A. novofumigatus can produce most of the same allergens, virulence, and pathogenicity factors as A. fumigatus, suggesting that A. novofumigatus could be as pathogenic as A. fumigatus Furthermore, SMs were linked to gene clusters based on biological and chemical knowledge and analysis, genome sequences, and predictive algorithms. We thus identify putative SM clusters for aflatoxin, chlorflavonin, and ochrindol in A. ochraceoroseus, A. campestris, and A. steynii, respectively, and novofumigatonin, ent-cycloechinulin, and epi-aszonalenins in A. novofumigatus Our study delivers six fungal genomes, showing the large diversity found in the Aspergillus genus; highlights the potential for discovery of beneficial or harmful SMs; and supports reports of A. novofumigatus pathogenicity. It also shows how biological, biochemical, and genomic information can be combined to identify genes involved in the biosynthesis of specific SMs.
Collapse
|
9
|
McCarthy CGP, Fitzpatrick DA. Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom. ADVANCES IN GENETICS 2017; 100:211-266. [PMID: 29153401 DOI: 10.1016/bs.adgen.2017.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Fungi are possibly the most diverse eukaryotic kingdom, with over a million member species and an evolutionary history dating back a billion years. Fungi have been at the forefront of eukaryotic genomics, and owing to initiatives like the 1000 Fungal Genomes Project the amount of fungal genomic data has increased considerably over the last 5 years, enabling large-scale comparative genomics of species across the kingdom. In this chapter, we first review fungal evolution and the history of fungal genomics. We then review in detail seven phylogenomic methods and reconstruct the phylogeny of 84 fungal species from 8 phyla using each method. Six methods have seen extensive use in previous fungal studies, while a Bayesian supertree method is novel to fungal phylogenomics. We find that both established and novel phylogenomic methods can accurately reconstruct the fungal kingdom. Finally, we discuss the accuracy and suitability of each phylogenomic method utilized.
Collapse
|
10
|
Zuo G, Hao B. Whole-genome-based phylogeny supports the objections against the reclassification of Eubacterium rectale to Agathobacter rectalis. Int J Syst Evol Microbiol 2016; 66:2451. [DOI: 10.1099/ijsem.0.001047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guanghong Zuo
- T-Life Research Center, Fudan University, Shanghai 200433, PR China
| | - Bailin Hao
- T-Life Research Center, Fudan University, Shanghai 200433, PR China
| |
Collapse
|
11
|
Zuo G, Hao B. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy. GENOMICS, PROTEOMICS & BIOINFORMATICS 2015; 13:321-31. [PMID: 26563468 PMCID: PMC4678791 DOI: 10.1016/j.gpb.2015.08.004] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/10/2015] [Indexed: 01/15/2023]
Abstract
A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.
Collapse
Affiliation(s)
- Guanghong Zuo
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China
| | - Bailin Hao
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.
| |
Collapse
|
12
|
Zuo G, Xu Z, Hao B. Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis. Life (Basel) 2015; 5:949-68. [PMID: 25789552 PMCID: PMC4390887 DOI: 10.3390/life5010949] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/06/2015] [Accepted: 03/09/2015] [Indexed: 11/29/2022] Open
Abstract
A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the Second Edition of Bergey's Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation.
Collapse
Affiliation(s)
- Guanghong Zuo
- Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.
| | - Zhao Xu
- Thermo Fisher Scientific, 200 Oyster Point Blvd, South San Francisco, CA 94080, USA.
| | - Bailin Hao
- Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.
| |
Collapse
|
13
|
|