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Wang X, Cui J, Gu Z, Guo L, Liu R, Guo Y, Qin N, Yang Y. Aged garlic oligosaccharides modulate host metabolism and gut microbiota to alleviate high-fat and high-cholesterol diet-induced atherosclerosis in ApoE -/- mice. Food Chem 2024; 463:141409. [PMID: 39326312 DOI: 10.1016/j.foodchem.2024.141409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 09/11/2024] [Accepted: 09/22/2024] [Indexed: 09/28/2024]
Abstract
Atherosclerosis (AS) is a cardiovascular disease caused by excessive accumulation of lipids in arterial walls. In this study, we developed an AS model in ApoE-/- mice using a high-fat, high-cholesterol diet and investigated the anti-AS mechanism of aged garlic oligosaccharides (AGOs) by focusing on the gut microbiota. Results revealed that AGOs exhibited significant anti-AS effects, reduced trimethylamine N-oxide levels from 349.9 to 189.2 ng/mL, and reduced aortic lipid deposition from 31.7 % to 9.5 %. AGOs significantly increased the levels of short-chain fatty acids in feces, in which acetic, propionic, and butyric acids were increased from 1.580, 0.364, and 0.469 mg/g to 2.233, 0.774, and 0.881 mg/g, respectively. An analysis of the gut microbiota indicated that AGOs restored alpha and beta diversity, decreased the Firmicutes/Bacteroidetes ratio, and promoted the dominance of the genus Akkermansia. A metagenomic analysis revealed that AGOs alleviated AS through the ABC transporter pathway and the lipopolysaccharide biosynthesis pathway.
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Affiliation(s)
- Xiaomin Wang
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Yuci 030619, China
| | - Jianglu Cui
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Yuci 030619, China
| | - Ziyao Gu
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Yuci 030619, China
| | - Lili Guo
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Yuci 030619, China
| | - Rui Liu
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Yuci 030619, China
| | - Yu Guo
- Shanxi Agricultural Products Quality and Safety Center, Taiyuan 030006, China
| | - Nan Qin
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Yuci 030619, China.
| | - Yukun Yang
- School of Life Science, Xinghuacun College (Shanxi Institute of Brewing Technology and Industry), Shanxi University, Taiyuan 030006, China.
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2
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Rottet S, Rourke LM, Pabuayon ICM, Phua SY, Yee S, Weerasooriya HN, Wang X, Mehra HS, Nguyen ND, Long BM, Moroney JV, Price GD. Engineering the cyanobacterial ATP-driven BCT1 bicarbonate transporter for functional targeting to C3 plant chloroplasts. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4926-4943. [PMID: 38776254 PMCID: PMC11349869 DOI: 10.1093/jxb/erae234] [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: 02/08/2024] [Accepted: 05/22/2024] [Indexed: 05/24/2024]
Abstract
The ATP-driven bicarbonate transporter 1 (BCT1) from Synechococcus is a four-component complex in the cyanobacterial CO2-concentrating mechanism. BCT1 could enhance photosynthetic CO2 assimilation in plant chloroplasts. However, directing its subunits (CmpA, CmpB, CmpC, and CmpD) to three chloroplast sub-compartments is highly complex. Investigating BCT1 integration into Nicotiana benthamiana chloroplasts revealed promising targeting strategies using transit peptides from the intermembrane space protein Tic22 for correct CmpA targeting, while the transit peptide of the chloroplastic ABCD2 transporter effectively targeted CmpB to the inner envelope membrane. CmpC and CmpD were targeted to the stroma by RecA and recruited to the inner envelope membrane by CmpB. Despite successful targeting, expression of this complex in CO2-dependent Escherichia coli failed to demonstrate bicarbonate uptake. We then used rational design and directed evolution to generate new BCT1 forms that were constitutively active. Several mutants were recovered, including a CmpCD fusion. Selected mutants were further characterized and stably expressed in Arabidopsis thaliana, but the transformed plants did not have higher carbon assimilation rates or decreased CO2 compensation points in mature leaves. While further analysis is required, this directed evolution and heterologous testing approach presents potential for iterative modification and assessment of CO2-concentrating mechanism components to improve plant photosynthesis.
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Affiliation(s)
- Sarah Rottet
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - Loraine M Rourke
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - Isaiah C M Pabuayon
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Su Yin Phua
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - Suyan Yee
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - Hiruni N Weerasooriya
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Xiaozhuo Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Himanshu S Mehra
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Nghiem D Nguyen
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - Benedict M Long
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, University of Newcastle, Callaghan, NSW 2308, Australia
| | - James V Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - G Dean Price
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
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Said AM, Mansour YE, Soliman RR, Islam R, Fatahala SS. Design, synthesis, molecular modeling, in vitro and in vivo biological evaluation of potent anthranilamide derivatives as dual P-glycoprotein and CYP3A4 inhibitors. Eur J Med Chem 2024; 273:116492. [PMID: 38762918 DOI: 10.1016/j.ejmech.2024.116492] [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: 03/09/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/21/2024]
Abstract
Paclitaxel (PTX) is considered the blockbuster chemotherapy treatment for cancer. Paclitaxel's (PTX) oral administration has proven to be extremely difficult, mostly because of its susceptibility to intestinal P-glycoprotein (P-gp) and cytochrome P450 (CYP3A4). The concurrent local inhibition of intestinal P-gp and CYP3A4 is a promising approach to improve the oral bioavailability of paclitaxel while avoiding potential unfavorable side effects of their systemic inhibition. Herein, we report the rational design and evaluation of novel dual potent inhibitors of P-gp and CYP3A4 using an anthranilamide derivative tariquidar as a starting point for their structural optimizations. Compound 14f, bearing N-imidazolylbenzyl side chain, was found to have potent and selective P-gp (EC50 = 28 nM) and CYP3A4 (IC50 = 223 nM) inhibitory activities with low absorption potential (Papp (A-to-B) <0.06). In vivo, inhibitor 14f improved the oral absorption of paclitaxel by 6 times in mice and by 30 times in rats as compared to vehicle, while 14f itself remained poorly absorbed. Compound 14f, possessing dual P-gp and CYP3A4 inhibitory activities, offered additional enhancement in paclitaxel oral absorption compared to tariquidar in mice. Evaluating the CYP effect of 14f on oral absorption of paclitaxel requires considering the variations in CYP expression between animal species. This study provides further medicinal chemistry advice on strategies for resolving concerns with the oral administration of chemotherapeutic agents.
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Affiliation(s)
- Ahmed M Said
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, BCC, Omaha, NE, 68198, USA; Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Ein-Helwan, Helwan, Cairo, 11795, Egypt; Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA.
| | - Yara E Mansour
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Ein-Helwan, Helwan, Cairo, 11795, Egypt
| | - Radwa R Soliman
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Ridwan Islam
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, BCC, Omaha, NE, 68198, USA
| | - Samar S Fatahala
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Ein-Helwan, Helwan, Cairo, 11795, Egypt.
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Hammes UZ, Pedersen BP. Structure and Function of Auxin Transporters. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:185-209. [PMID: 38211951 DOI: 10.1146/annurev-arplant-070523-034109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Auxins, a group of central hormones in plant growth and development, are transported by a diverse range of transporters with distinct biochemical and structural properties. This review summarizes the current knowledge on all known auxin transporters with respect to their biochemical and biophysical properties and the methods used to characterize them. In particular, we focus on the recent advances that were made concerning the PIN-FORMED family of auxin exporters. Insights derived from solving their structures have improved our understanding of the auxin export process, and we discuss the current state of the art on PIN-mediated auxin transport, including the use of biophysical methods to examine their properties. Understanding the mechanisms of auxin transport is crucial for understanding plant growth and development, as well as for the development of more effective strategies for crop production and plant biotechnology.
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Affiliation(s)
- Ulrich Z Hammes
- School of Life Sciences, Plant Systems Biology, Technical University of Munich, Freising, Germany;
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Alcorlo M, Martínez-Caballero S, Li J, Sham LT, Luo M, Hermoso JA. Modulation of the lytic apparatus by the FtsEX complex within the bacterial division machinery. FEBS Lett 2024. [PMID: 38849310 DOI: 10.1002/1873-3468.14953] [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: 04/25/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024]
Abstract
The FtsEX membrane complex constitutes an essential component of the ABC transporter superfamily, widely distributed among bacterial species. It governs peptidoglycan degradation for cell division, acting as a signal transmitter rather than a substrate transporter. Through the ATPase activity of FtsE, it facilitates signal transmission from the cytosol across the membrane to the periplasm, activating associated peptidoglycan hydrolases. This review concentrates on the latest structural advancements elucidating the architecture of the FtsEX complex and its interplay with lytic enzymes or regulatory counterparts. The revealed three-dimensional structures unveil a landscape wherein a precise array of intermolecular interactions, preserved across diverse bacterial species, afford meticulous spatial and temporal control over the cell division process.
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Affiliation(s)
- Martín Alcorlo
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Siseth Martínez-Caballero
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jianwei Li
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
- Department of Biological Sciences, Center for Bioimaging Sciences, National University of Singapore, Singapore
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Min Luo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
- Department of Biological Sciences, Center for Bioimaging Sciences, National University of Singapore, Singapore
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Blas Cabrera", Consejo Superior de Investigaciones Científicas, Madrid, Spain
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6
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Kasten A, Cascorbi I. Understanding the impact of ABCG2 polymorphisms on drug pharmacokinetics: focus on rosuvastatin and allopurinol. Expert Opin Drug Metab Toxicol 2024; 20:519-528. [PMID: 38809523 DOI: 10.1080/17425255.2024.2362184] [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: 03/25/2024] [Accepted: 05/28/2024] [Indexed: 05/30/2024]
Abstract
INTRODUCTION In addition to the well-established understanding of the pharmacogenetics of drug-metabolizing enzymes, there is growing data on the effects of genetic variation in drug transporters, particularly ATP-binding cassette (ABC) transporters. However, the evidence that these genetic variants can be used to predict drug effects and to adjust individual dosing to avoid adverse events is still limited. AREAS COVERED This review presents a summary of the current literature from the PubMed database as of February 2024 regarding the impact of genetic variants on ABCG2 function and their relevance to the clinical use of the HMG-CoA reductase inhibitor rosuvastatin and the xanthine oxidase inhibitor allopurinol. EXPERT OPINION Although there are pharmacogenetic guidelines for the ABCG2 missense variant Q141K, there is still some conflicting data regarding the clinical benefits of these recommendations. Some caution appears to be warranted in homozygous ABCG2 Q141K carriers when rosuvastatin is administered at higher doses and such information is already included in the drug label. The benefit of dose adaption to lower possible side effects needs to be evaluated in prospective clinical studies.
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Affiliation(s)
- Anne Kasten
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Kiel, Germany
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Aktar N, Mannan E, Kabir SMT, Hasan R, Hossain MS, Ahmed R, Ahmed B, Islam MS. Comparative metagenomics and microbial dynamics of jute retting environment. Int Microbiol 2024; 27:113-126. [PMID: 37204507 DOI: 10.1007/s10123-023-00377-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Jute, eco-friendly natural fiber, depends on conventional water-based microbial retting process that suffers from the production of low-quality fiber, restricting its diversified applications. The efficiency of water retting of jute depends on plant polysaccharide fermenting pectinolytic microorganisms. Understanding the phase difference in retting microbial community composition is crucial to provide knowledge on the functions of each member of microbiota for the improvement of retting and fiber quality. The retting microbiota profiling of jute was commonly performed previously using only one retting phase with culture-dependent methods which has limited coverage and accuracy. Here, for the first we have analyzed jute retting water through WGS metagenome approach in three phases (pre-retting, aerobic retting, and anaerobic retting phases) and characterized the microbial communities both culturable and non-culturable along with their dynamics with the fluctuation of oxygen availability. Our analysis revealed a total of 25.99 × 104 unknown proteins (13.75%), 16.18 × 105 annotated proteins (86.08%), and 32.68 × 102 ribosomal RNA (0.17%) in the pre-retting phase, 15.12 × 104 unknown proteins (8.53%), 16.18 × 105 annotated proteins (91.25%), and 38.62 × 102 ribosomal RNA (0.22%) in the aerobic retting phase, and 22.68 × 102 ribosomal RNA and 80.14 × 104 (99.72%) annotated protein in the anaerobic retting phase. Taxonomically, we identified 53 different phylotypes in the retting environment, with Proteobacteria being the dominant taxa comprising over 60% of the population. We have identified 915 genera from Archaea, Viruses, Bacteria, and Eukaryota in the retting habitat, with anaerobic or facultative anaerobic pectinolytic microflora being enriched in the anoxic, nutrient-rich retting niche, such as Aeromonas (7%), Bacteroides (3%), Clostridium (6%), Desulfovibrio (4%), Acinetobacter (4%), Enterobacter (1%), Prevotella (2%), Acidovorax (3%), Bacillus (1%), Burkholderia (1%), Dechloromonas (2%), Caulobacter (1%) and Pseudomonas (7%). We observed an increase in the expression of 30 different KO functional level 3 pathways in the final retting stage compared to the middle and pre-retting stages. The main functional differences among the retting phases were found to be related to nutrient absorption and bacterial colonization. These findings reveal the bacterial groups that are involved in fiber retting different phases and will facilitate to develop future phase-specific microbial consortia for the improvement of jute retting process.
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Affiliation(s)
- Nasima Aktar
- Basic and Applied Research on Jute, Dhaka, Bangladesh.
| | | | | | - Rajnee Hasan
- Basic and Applied Research on Jute, Dhaka, Bangladesh
| | - Md Sabbir Hossain
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Rasel Ahmed
- Basic and Applied Research on Jute, Dhaka, Bangladesh
| | - Borhan Ahmed
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
| | - Md Shahidul Islam
- Basic and Applied Research on Jute, Dhaka, Bangladesh
- Bangladesh Jute Research Institute, Dhaka, Bangladesh
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Liu Y, Chen Y, Yue X, Liu Y, Ning J, Li L, Wu J, Luo X, Zhang S. Proteomics and Metabolomics Analysis Reveal the Regulation Mechanism of Linoleate Isomerase Activity and Function in Propionibacterium acnes. ACS OMEGA 2024; 9:1643-1655. [PMID: 38222669 PMCID: PMC10785318 DOI: 10.1021/acsomega.3c08243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 01/16/2024]
Abstract
Conjugated linoleic acid (CLA) holds significant application prospects due to its anticancer, anti-atherosclerosis, lipid-lowering, weight-loss, and growth-promoting functions. The key to its efficient production lies in optimizing the biocatalytic performance of linoleic acid isomerase (LAI). Here, we constructed a Propionibacterium acnes mutant library and screened positive mutants with high linoleate isomerase activity. The proteomics and metabolomics were used to explore the mechanism in the regulation of linoleic acid isomerase activity. High-throughput proteomics revealed 104 differentially expressed proteins unique to positive mutant strains of linoleic acid isomerase of which 57 were upregulated and 47 were downregulated. These differentially expressed proteins were primarily involved in galactose metabolism, the phosphotransferase system, starch metabolism, and sucrose metabolism. Differential metabolic pathways were mainly enriched in amino acid biosynthesis, including glutamate metabolism, the Aminoacyl-tRNA biosynthesis pathway, and the ABC transporter pathway. The upregulated metabolites include dl-valine and Acetyl coA, while the downregulated metabolites include Glutamic acid and Phosphoenolpyruvate. Overall, the activity of linoleic acid isomerase in the mutant strain was increased by the regulation of key proteins involved in galactose metabolism, sucrose metabolism, and the phosphotransferase system. This study provides a theoretical basis for the development of high-yield CLA food.
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Affiliation(s)
- Ying Liu
- College
of Food Science, Shenyang Agricultural University, Shenyang 110000, China
| | - Yeping Chen
- College
of Food Science, Shenyang Agricultural University, Shenyang 110000, China
| | - Xiqing Yue
- College
of Food Science, Shenyang Agricultural University, Shenyang 110000, China
| | - Yingying Liu
- College
of Food Science, Shenyang Agricultural University, Shenyang 110000, China
| | - Jianting Ning
- College
of Food Science, Shenyang Agricultural University, Shenyang 110000, China
| | - Libo Li
- College
of Food Science, Shenyang Agricultural University, Shenyang 110000, China
| | - Junrui Wu
- College
of Food Science, Shenyang Agricultural University, Shenyang 110000, China
| | - Xue Luo
- College
of Food Science, Shenyang Agricultural University, Shenyang 110000, China
| | - Shuang Zhang
- College
of Food Science, Northeast Agricultural
University, Harbin 150000, China
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Tjo H, Conway JM. Sugar transport in thermophiles: Bridging lignocellulose deconstruction and bioconversion. J Ind Microbiol Biotechnol 2024; 51:kuae020. [PMID: 38866721 PMCID: PMC11212667 DOI: 10.1093/jimb/kuae020] [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: 03/14/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024]
Abstract
Biomass degrading thermophiles play an indispensable role in building lignocellulose-based supply chains. They operate at high temperatures to improve process efficiencies and minimize mesophilic contamination, can overcome lignocellulose recalcitrance through their native carbohydrate-active enzyme (CAZyme) inventory, and can utilize a wide range of sugar substrates. However, sugar transport in thermophiles is poorly understood and investigated, as compared to enzymatic lignocellulose deconstruction and metabolic conversion of sugars to value-added chemicals. Here, we review the general modes of sugar transport in thermophilic bacteria and archaea, covering the structural, molecular, and biophysical basis of their high-affinity sugar uptake. We also discuss recent genetic studies on sugar transporter function. With this understanding of sugar transport, we discuss strategies for how sugar transport can be engineered in thermophiles, with the potential to enhance the conversion of lignocellulosic biomass into renewable products. ONE-SENTENCE SUMMARY Sugar transport is the understudied link between extracellular biomass deconstruction and intracellular sugar metabolism in thermophilic lignocellulose bioprocessing.
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Affiliation(s)
- Hansen Tjo
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jonathan M Conway
- Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ 08544, USA
- High Meadows Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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Yuan Y, Xiang Z, Xia Y, Xie J, Jiang X, Lu Z. The role of ATP binding cassette (ABC) transporters in breast cancer: Evaluating prognosis, predicting immunity, and guiding treatment. Channels (Austin) 2023; 17:2273247. [PMID: 37905302 PMCID: PMC10761142 DOI: 10.1080/19336950.2023.2273247] [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: 04/29/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023] Open
Abstract
Breast cancer is currently the most prevalent form of cancer worldwide. Nevertheless, there remains limited clarity regarding our understanding of the tumor microenvironment and metabolic characteristics associated with it. ATP-binding cassette (ABC) transporters are the predominant transmembrane transporters found in organisms. Therefore, it is essential to investigate the role of ABC transporters in breast cancer. Transcriptome data from breast cancer patients were downloaded from the TCGA database. ABC transporter-related genes were obtained from the Genecards database. By LASSO regression, ABC-associated prognostic signature was constructed in breast cancer. Subsequently, immune microenvironment analysis was performed. Finally, cell experiments were performed to verify the function of ABCB7 in the breast cancer cell lines MDA-MB-231 and MCF-7. Using the ABC transporter-associated signature, we calculated a risk score for each breast cancer patient. Patients with breast cancer were subsequently categorized into high-risk and low-risk groups, utilizing the median risk score as the threshold. Notably, patients in the high-risk group exhibited significantly worse prognosis (P<0.05). Additionally, differences were observed in terms of immune cell infiltration levels, immune correlations, and gene expression of immune checkpoints between the two groups. Functional experiments conducted on breast cancer cell lines MDA-MB-231 and MCF-7 demonstrated that ABCB7 knockdown significantly diminished cell activity, proliferation, invasion, and migration. These findings emphasize the significance of understanding ABC transporter-mediated metabolic and transport characteristics in breast cancer, offering promising directions for further research and potential therapeutic interventions.
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Affiliation(s)
- Yuan Yuan
- Department of Laboratory Medicine, The Seventh People’s Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhouhong Xiang
- Department of Laboratory Medicine, The Seventh People’s Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuhua Xia
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, Hubei, China
| | - Jiaheng Xie
- Department of Plastic and Cosmetic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiudi Jiang
- Department of Laboratory Medicine, The Seventh People’s Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhicheng Lu
- Department of Laboratory Medicine, The Seventh People’s Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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11
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Mall MS, Shah S, Singh S, Singh N, Singh N, Vaish S, Gupta D. Genome-wide identification and characterization of ABC transporter superfamily in the legume Cajanus cajan. J Appl Genet 2023; 64:615-644. [PMID: 37624461 DOI: 10.1007/s13353-023-00774-8] [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: 03/20/2023] [Revised: 07/17/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
Plant ATP-binding cassette (ABC) protein family is the largest multifunctional highly conserved protein superfamily that transports diverse substrates across biological membranes by the hydrolysis of ATP and is also the part of the several other biological processes like cellular detoxification, growth and development, stress biology, and signaling processes. In the agriculturally important legume crop Cajanus cajan, a genome-wide identification and characterization of the ABC gene family was carried out. A total of 159 ABC genes were identified that belong to eight canonical classes CcABCA to CcABCG and CcABCI based on the phylogenetic analysis. The number of genes was highest in CcABCG followed by CcABCC and CcABCB class. A total of 85 CcABC genes were found on 11 chromosomes and 74 were found on scaffold. Tandem duplication was the major driver of CcABC gene family expansion. The dN/dS ratio revealed the purifying selection. The phylogenetic analysis revealed class-specific eight superclades which reflect their functional importance. The largest clade was found to be CcABCG which reflects their functional significance. CcABC proteins were mainly basic in nature and found to be localized in the plasma membrane. The secondary structure prediction revealed the dominance of α-helix. The canonical transmembrane and nucleotide binding domain, signature motif LSSGQ, Walker A, Walker B region, and Q loop were also identified. A class-specific exon-intron pattern was also observed. In addition to core elements, different cis-acting regulatory elements like stress, hormone, and cellular responsive were also identified. Expression profiling of CcABC genes at various developmental stages of different anatomical tissues was performed and it was noticed that CcABCF3, CcABCF4, CcABCF5, CcABCG66, and CcABCI3 had the highest expression. The results of the current study endow us with the further functional analysis of Cajanus ABC in the future.
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Affiliation(s)
- Mridula Sanjana Mall
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Shreya Shah
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Shivani Singh
- Experiome Biotech Private Limited, B1-517, Vijaypur Colony, DLF MyPAD, Vibhutikhand, Gomtinagar, Lucknow, Uttar Pradesh, 226010, India
| | - Namita Singh
- Experiome Biotech Private Limited, B1-517, Vijaypur Colony, DLF MyPAD, Vibhutikhand, Gomtinagar, Lucknow, Uttar Pradesh, 226010, India
| | - Nootan Singh
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Swati Vaish
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India
| | - Divya Gupta
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, -Deva Road, Barabanki, Lucknow, Uttar Pradesh, 225003, India.
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12
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Shehzad M, Bodlah I, Siddiqui JA, Bodlah MA, Fareen AGE, Islam W. Recent insights into pesticide resistance mechanisms in Plutella xylostella and possible management strategies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:95296-95311. [PMID: 37606784 DOI: 10.1007/s11356-023-29271-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
Insects are incredibly successful and diverse organisms, but they also pose a significant threat to agricultural crops, causing potential losses of up to US$470 billion. Among these pests, Plutella xylostella (Linnaeus), a devastating insect that attacks cruciferous vegetables, alone results in monetary losses of around US$4-5 billion worldwide. While insecticides have effectively protected plants under field conditions, their use comes with various environmental and mammalian hazards. Additionally, insects are developing resistance to commonly used insecticides, rendering management strategies less effective. Arthropods employ a range of behavioral and biochemical mechanisms to cope with harmful chemicals, which contribute to the development of resistance. Understanding these mechanisms is crucial for addressing the issue of resistance. It is imperative to integrate strategies that can delay the development of resistance and enhance the efficiency of insecticides. Therefore, we present an overview of insecticide resistance in insects, focusing on P. xylostella, to provide insights into the current resistance status of this pest and propose tactics that can improve the effectiveness of insecticides.
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Affiliation(s)
- Muhammad Shehzad
- Department of Entomology, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - Imran Bodlah
- Department of Entomology, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - Junaid Ali Siddiqui
- College of Agriculture, College of Life Science, Guizhou University, Guiyang, 550025, China
| | - Muhammad Adnan Bodlah
- Fareed Biodiversity Conservation Centre, Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, Pakistan
| | - Ammara Gull E Fareen
- Department of Environmental Sciences, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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13
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Ashique S, Garg A, Hussain A, Farid A, Kumar P, Taghizadeh‐Hesary F. Nanodelivery systems: An efficient and target-specific approach for drug-resistant cancers. Cancer Med 2023; 12:18797-18825. [PMID: 37668041 PMCID: PMC10557914 DOI: 10.1002/cam4.6502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/16/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Cancer treatment is still a global health challenge. Nowadays, chemotherapy is widely applied for treating cancer and reducing its burden. However, its application might be in accordance with various adverse effects by exposing the healthy tissues and multidrug resistance (MDR), leading to disease relapse or metastasis. In addition, due to tumor heterogeneity and the varied pharmacokinetic features of prescribed drugs, combination therapy has only shown modestly improved results in MDR malignancies. Nanotechnology has been explored as a potential tool for cancer treatment, due to the efficiency of nanoparticles to function as a vehicle for drug delivery. METHODS With this viewpoint, functionalized nanosystems have been investigated as a potential strategy to overcome drug resistance. RESULTS This approach aims to improve the efficacy of anticancer medicines while decreasing their associated side effects through a range of mechanisms, such as bypassing drug efflux, controlling drug release, and disrupting metabolism. This review discusses the MDR mechanisms contributing to therapeutic failure, the most cutting-edge approaches used in nanomedicine to create and assess nanocarriers, and designed nanomedicine to counteract MDR with emphasis on recent developments, their potential, and limitations. CONCLUSIONS Studies have shown that nanoparticle-mediated drug delivery confers distinct benefits over traditional pharmaceuticals, including improved biocompatibility, stability, permeability, retention effect, and targeting capabilities.
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Affiliation(s)
- Sumel Ashique
- Department of PharmaceuticsPandaveswar School of PharmacyPandaveswarIndia
| | - Ashish Garg
- Guru Ramdas Khalsa Institute of Science and Technology, PharmacyJabalpurIndia
| | - Afzal Hussain
- Department of Pharmaceutics, College of PharmacyKing Saud UniversityRiyadhSaudi Arabia
| | - Arshad Farid
- Gomal Center of Biochemistry and BiotechnologyGomal UniversityDera Ismail KhanPakistan
| | - Prashant Kumar
- Teerthanker Mahaveer College of PharmacyTeerthanker Mahaveer UniversityMoradabadIndia
- Department of Pharmaceutics, Amity Institute of PharmacyAmity University Madhya Pradesh (AUMP)GwaliorIndia
| | - Farzad Taghizadeh‐Hesary
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of MedicineIran University of Medical SciencesTehranIran
- Clinical Oncology DepartmentIran University of Medical SciencesTehranIran
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14
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Nagy EZ, Kovács ÁB, Wehmann E, Bekő K, Földi D, Bányai K, Kreizinger Z, Gyuranecz M. Phenotypic and genetic insights into efflux pump mechanism in Mycoplasma anserisalpingitidis. Front Microbiol 2023; 14:1216893. [PMID: 37502405 PMCID: PMC10371760 DOI: 10.3389/fmicb.2023.1216893] [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: 05/04/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
Introduction Mycoplasma anserisalpingitidis is one of the most important waterfowl-pathogenic mycoplasmas. Due to inadequate antibiotic treatment, many strains with high minimal inhibitory concentration (MIC) values for multiple drugs have been isolated lately. Decreased antibiotic susceptibility in several Mycoplasma species are known to be associated with mutations in topoisomerase and ribosomal genes, but other strategies such as active efflux pump mechanisms were also described. The scope of this study was the phenotypic and genetic characterization of the active efflux mechanism in M. anserisalpingitidis. Methods We measured the MIC values in the presence and absence of different efflux pump inhibitors (EPIs), such as carbonyl cyanide m-chlorophenylhydrazine (CCCP), orthovanadate (OV), and reserpine (RSP). Moreover, bioinformatic tools were utilized to detect putative regulatory sequences of membrane transport proteins coding genes, while comparative genome analysis was performed to reveal potential markers of antibiotic resistance. Results Out of the three examined EPIs, CCCP decreased the MICs at least two-fold below the original MICs (in 23 cases out of 36 strains). In the presence of OV or RSP, MIC value differences could be seen only if modified dilution series (10% decrease steps were used instead of two-fold dilutions) were applied (in 24/36 cases with OV and 9/36 with RSP). During comparative genome analysis, non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in genes encoding ABC membrane transport proteins, which were displayed in higher percentages in M. anserisalpingitidis strains with increased MICs. In terms of other genes, a nsSNP was identified in DNA gyrase subunit A (gyrA) gene which can be related to decreased susceptibility to enrofloxacin. The present study is the first to highlight the importance of efflux pump mechanisms in M. anserisalpingitidis. Discussion Considering the observed effects of the EPI CCCP against this bacterium, it can be assumed, that the use of EPIs would increase the efficiency of targeted antibiotic therapy in the future control of this pathogen. However, further research is required to obtain a more comprehensive understanding of efflux pump mechanism in this bacterium.
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Affiliation(s)
- Eszter Zsófia Nagy
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Áron Botond Kovács
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Enikő Wehmann
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Katinka Bekő
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Dorottya Földi
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
| | - Zsuzsa Kreizinger
- Veterinary Medical Research Institute, Budapest, Hungary
- MolliScience Kft., Biatorbágy, Hungary
| | - Miklós Gyuranecz
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- MolliScience Kft., Biatorbágy, Hungary
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
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15
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Chen DB, Xia RX, Li Q, Li YP, Cao HY, Liu YQ. Genome-Wide Identification of Detoxification Genes in Wild Silkworm Antheraea pernyi and Transcriptional Response to Coumaphos. Int J Mol Sci 2023; 24:ijms24119775. [PMID: 37298726 DOI: 10.3390/ijms24119775] [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: 03/30/2023] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023] Open
Abstract
For a half-century, the commercial wild silkworm, Antheraea pernyi, has been protected by coumaphos, which is an internal organophosphorus insecticide used to kill the potential parasitic fly larvae inside. Knowledge about the detoxification genes of A. pernyi as well as the detoxification mechanism for this species remains severely limited. In this study, we identified 281 detoxification genes (32 GSTs, 48 ABCs, 104 CYPs, and 97 COEs) in the genome of this insect, which are unevenly distributed over 46 chromosomes. When compared to the domesticated silkworm, Bombyx mori, a lepidopteran model species, A. pernyi has a similar number of ABCs, but a greater number of GSTs, CYPs, and COEs. By transcriptome-based expression analysis, we found that coumaphos at a safe concentration level significantly changed the pathways related to ATPase complex function and the transporter complex in A. pernyi. KEGG functional enrichment analysis indicated that protein processing in the endoplasmic reticulum was the most affected pathway after coumaphos treatment. Finally, we identified four significantly up-regulated detoxification genes (ABCB1, ABCB3, ABCG11, and ae43) and one significantly down-regulated detoxification gene (CYP6AE9) in response to coumaphos treatment, suggesting that these five genes may contribute to detoxification of coumaphos in A. pernyi. Our study provides the first set of detoxification genes for wild silkworms from Saturniidae and highlights the importance of detoxification gene repertoire in insect pesticide tolerance.
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Affiliation(s)
- Dong-Bin Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Run-Xi Xia
- College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Qun Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Yu-Ping Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Hui-Ying Cao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Yan-Qun Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
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16
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Chen D, Feng Q, Zhang Y. Enrichment and response of iron-metabolizing microorganisms and metabolic genes in the contaminated area of stratified stacking coal gangue dumps, Northern China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:63603-63619. [PMID: 37046168 DOI: 10.1007/s11356-023-26775-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023]
Abstract
In the Xishan coalfield of northern China, the stratified stacking of soil and gangue was applied to limit the acid pollution from high-sulfur coal gangue. In this study, we found that stratified stacking can effectively neutralize the acidity, with the pH value of gangue-leaching water being 6.02-8.13. In contrast to the acidic contaminated area, most of the microorganisms in the study area sediment were neutrophilic, with the main genera being Arthrobacter, Pseudorhodobacter, Pseudomonas, and Rhodoferax. A variety of iron- and sulfur-metabolizing bacteria was discovered in the gangue-leaching sediment, with the total relative abundance ranging from 4.20 to 23.75%, of which the iron-reducing bacteria (FeRB) accounted for the highest percentage. The distributions of these functional microorganisms in the samples were significantly influenced by Fe and S. The co-occurrence network analysis revealed a significant positive correlation between the iron- and sulfur-metabolizing bacteria in the sediment (93.75%), indicating a strong reciprocal symbiotic relationship between these bacteria. The iron and sulfur metabolism genes in the sediment were predicted and compared based on the Tax4Fun functional prediction method. Results showed that functional genes related to iron metabolism were highly expressed in the gangue-leaching sediment. This study enhances the understanding of iron and sulfur metabolism in gangue-leaching contaminated areas.
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Affiliation(s)
- Di Chen
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, No.1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, No.1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
| | - Qiyan Feng
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, No.1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China.
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, No.1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China.
| | - Yun Zhang
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, No.1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, No.1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
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17
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Bhandari P, Hill JE. Transport and Utilization of Glycogen Breakdown Products by Gardnerella spp. from the Human Vaginal Microbiome. Microbiol Spectr 2023; 11:e0443522. [PMID: 36920187 PMCID: PMC10101108 DOI: 10.1128/spectrum.04435-22] [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: 11/02/2022] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
Multiple Gardnerella species frequently cooccur in vaginal microbiomes, and several factors, including competition for nutrients such as glycogen could determine their population structure. Although Gardnerella spp. can hydrolyze glycogen to produce glucose, maltose, maltotriose, and maltotetraose, how these sugars are transported and utilized for growth is unknown. We determined the distribution of genes encoding transporter proteins associated with the uptake of glucose, maltose, and malto-oligosaccharides and maltodextrins among Gardnerella species. A total of five different ABC transporters were identified in Gardnerella spp. of which MusEFGK2I and MalXFGK were conserved across all 15 Gardnerella isolates. RafEFGK and TMSP (trehalose, maltose, sucrose, and palatinose) operons were specific to G. vaginalis while the MalEFG transporter was identified in G. leopoldii only. Although no glucose specific sugar-symporters were identified, putative "glucose/galactose porters" and components of a phosphotransferase system were identified. In laboratory experiments, all Gardnerella isolates grew more in the presence of glucose, maltose, maltotriose, and maltotetraose compared to unsupplemented media. In addition, most isolates (10/15) showed significantly more growth on maltotetraose compared to glucose (Kruskal Wallis, P < 0.05) suggesting their preference for longer chain malto-oligosaccharides. Our findings show that although putative MusEFGK2I and MalXFGK transporters are found in all Gardnerella spp., some species-specific transporters are also present. Observed distribution of genes encoding transporter systems was consistent with laboratory observations that Gardnerella spp. grow better on longer chain malto-oligosaccharides. IMPORTANCE Increased abundance of Gardnerella spp. is a diagnostic characteristic of bacterial vaginosis, an imbalance in the human vaginal microbiome associated with troubling symptoms and negative reproductive health outcomes, including increased transmission of sexually transmitted infections and preterm birth. Competition for nutrients is likely an important factor in causing dramatic shifts in the vaginal microbial community. Gardnerella produces enzymes to digest glycogen, an important nutrient source for vaginal bacteria, but little is known about the mechanisms in Gardnerella for uptake of the products of this digestion, or whether Gardnerella use some or all of the products. Our results indicate that Gardnerella may have evolved to preferentially use a subset of the glycogen breakdown products, which would help them reduce direct competition with some other bacteria in the vagina.
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Affiliation(s)
- Pashupati Bhandari
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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18
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Teoh CP, Lavin P, Yusof NA, González-Aravena M, Najimudin N, Cheah YK, Wong CMVL. Transcriptomics analysis provides insights into the heat adaptation strategies of an Antarctic bacterium, Cryobacterium sp. SO1. Polar Biol 2023. [DOI: 10.1007/s00300-023-03115-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
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19
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Ang’ang’o LM, Herren JK, Tastan Bishop Ö. Structural and Functional Annotation of Hypothetical Proteins from the Microsporidia Species Vittaforma corneae ATCC 50505 Using in silico Approaches. Int J Mol Sci 2023; 24:3507. [PMID: 36834914 PMCID: PMC9960886 DOI: 10.3390/ijms24043507] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/25/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Microsporidia are spore-forming eukaryotes that are related to fungi but have unique traits that set them apart. They have compact genomes as a result of evolutionary gene loss associated with their complete dependency on hosts for survival. Despite having a relatively small number of genes, a disproportionately high percentage of the genes in microsporidia genomes code for proteins whose functions remain unknown (hypothetical proteins-HPs). Computational annotation of HPs has become a more efficient and cost-effective alternative to experimental investigation. This research developed a robust bioinformatics annotation pipeline of HPs from Vittaforma corneae, a clinically important microsporidian that causes ocular infections in immunocompromised individuals. Here, we describe various steps to retrieve sequences and homologs and to carry out physicochemical characterization, protein family classification, identification of motifs and domains, protein-protein interaction network analysis, and homology modelling using a variety of online resources. Classification of protein families produced consistent findings across platforms, demonstrating the accuracy of annotation utilizing in silico methods. A total of 162 out of 2034 HPs were fully annotated, with the bulk of them categorized as binding proteins, enzymes, or regulatory proteins. The protein functions of several HPs from Vittaforma corneae were accurately inferred. This improved our understanding of microsporidian HPs despite challenges related to the obligate nature of microsporidia, the absence of fully characterized genes, and the lack of homologous genes in other systems.
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Affiliation(s)
- Lilian Mbaisi Ang’ang’o
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140, South Africa
| | - Jeremy Keith Herren
- International Centre of Insect Physiology and Ecology (icipe), Nairobi P.O. Box 30772-00100, Kenya
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140, South Africa
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20
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Sodium hydroxide-induced Weissella kimchii ghosts (WKGs) as immunostimulant. Mol Cell Toxicol 2022. [DOI: 10.1007/s13273-022-00321-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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21
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Secretome Analysis of the Plant Biostimulant Bacteria Strains Bacillus subtilis (EB2004S) and Lactobacillus helveticus (EL2006H) in Response to pH Changes. Int J Mol Sci 2022; 23:ijms232315144. [PMID: 36499471 PMCID: PMC9739546 DOI: 10.3390/ijms232315144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
It is well-known that there is a high frequency of plant-growth-promoting strains in Bacillus subtilis and that these can be effective under both stressful and stress-free conditions. There are very few studies of this activity in the case of Lactobacillus helveticus. In this study, the effects of pH on the secretome (proteins) in the cell-free supernatants of two bacterial strains were evaluated. The bacteria were cultured at pH 5, 7 and 8, and their secretome profiles were analyzed, with pH 7 (optimal growth pH) considered as the "control". The results showed that acidity (lower pH 5) diminishes the detectable production of most of the secretome proteins, whereas alkalinity (higher pH 8) increases the detectable protein production. At pH 5, five (5) new proteins were produced by L. helveticus, including class A sortase, fucose-binding lectin II, MucBP-domain-containing protein, SLAP-domain-containing protein and hypothetical protein LHEJCM1006_11110, whereas for B. subtilis, four (4) types of proteins were uniquely produced (p ≤ 0.05), including helicase-exonuclease AddAB subunit AddB, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase, a cluster of ABC-F family ATP-binding-cassette-domain-containing proteins and a cluster of excinuclease ABC (subunit B). At pH 8, Bacillus subtilis produced 56 unique proteins. Many of the detected proteins were involved in metabolic processes, whereas the others had unknown functions. The unique and new proteins with known and unknown functions suggest potential the acclimatization of the microbes to pH stress.
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Grigoreva TA, Sagaidak AV, Novikova DS, Tribulovich VG. Implication of ABC transporters in non-proliferative diseases. Eur J Pharmacol 2022; 935:175327. [DOI: 10.1016/j.ejphar.2022.175327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/28/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022]
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Cai H, Zhang H, Guo DH, Wang Y, Gu J. Genomic Data Mining Reveals Abundant Uncharacterized Transporters in Coccidioides immitis and Coccidioides posadasii. J Fungi (Basel) 2022; 8:jof8101064. [PMID: 36294626 PMCID: PMC9604845 DOI: 10.3390/jof8101064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/01/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Coccidioides immitis and Coccidioides posadasii are causative agents of coccidioidomycosis, commonly known as Valley Fever. The increasing Valley Fever cases in the past decades, the expansion of endemic regions, and the rising azole drug-resistant strains have underscored an urgent need for a better understanding of Coccidioides biology and new antifungal strategies. Transporters play essential roles in pathogen survival, growth, infection, and adaptation, and are considered as potential drug targets. However, the composition and roles of transport machinery in Coccidioides remain largely unknown. In this study, genomic data mining revealed an abundant, uncharacterized repertoire of transporters in Coccidioides genomes. The catalog included 1288 and 1235 transporter homologs in C. immitis and C. posadasii, respectively. They were further annotated to class, subclass, family, subfamily and range of substrates based on the Transport Classification (TC) system. They may play diverse roles in nutrient uptake, metabolite secretion, ion homeostasis, drug efflux, or signaling. This study represents an initial effort for a systems-level characterization of the transport machinery in these understudied fungal pathogens.
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Affiliation(s)
- Hong Cai
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Daniel H. Guo
- Strake Jesuit College Preparatory, Houston, TX 77036, USA
| | - Yufeng Wang
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Correspondence: (Y.W.); (J.G.)
| | - Jianying Gu
- Department of Biology, College of Staten Island, City University of New York, Staten Island, New York, NY 10314, USA
- Correspondence: (Y.W.); (J.G.)
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Hoeger AL, Jehmlich N, Kipping L, Griehl C, Noll M. Associated bacterial microbiome responds opportunistic once algal host Scenedesmus vacuolatus is attacked by endoparasite Amoeboaphelidium protococcarum. Sci Rep 2022; 12:13187. [PMID: 35915148 PMCID: PMC9343445 DOI: 10.1038/s41598-022-17114-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/20/2022] [Indexed: 11/09/2022] Open
Abstract
The interactions of microalgae and their associated microbiomes have come to the fore of applied phycological research in recent years. However, the functional mechanisms of microalgal interactions remain largely unknown. Here, we examine functional protein patterns of the microalgae Scenedesmus vacuolatus and its associated bacterial community during algal infection by the endoparasite Amoeboaphelidium protococcarum. We performed metaproteomics analyses of non-infected (NI) and aphelid-infected (AI) S.vacuolatus cultures to investigate underlying functional and physiological changes under infectious conditions. We observed an increase in bacterial protein abundance as well as a severe shift of bacterial functional patterns throughout aphelid-infection in comparison to NI treatment. Most of the bacterial proteins (about 55%) upregulated in AI were linked to metabolism and transport of amino acids, lipids, coenzymes, nucleotides and carbohydrates and to energy production. Several proteins associated with pathogenic bacterial-plant interactions showed higher protein abundance levels in AI treatment. These functional shifts indicate that associated bacteria involved in commensalistic or mutualistic interactions in NI switch to opportunistic lifestyles and facilitate pathogenic or saprotrophic traits in AI treatment. In summary, the native bacterial microbiome adapted its metabolism to algal host die off and is able to metabolize nutrients from injured cells or decompose dead cellular material.
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Affiliation(s)
- Anna-Lena Hoeger
- Competence Center Algae Biotechnology, Anhalt University of Applied Sciences, Koethen, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Permoserstr. 15, 04318, Leipzig, Germany
| | - Lydia Kipping
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Permoserstr. 15, 04318, Leipzig, Germany
| | - Carola Griehl
- Competence Center Algae Biotechnology, Anhalt University of Applied Sciences, Koethen, Germany
| | - Matthias Noll
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany. .,Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany.
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25
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Guffick C, Hsieh PY, Ali A, Shi W, Howard J, Chinthapalli DK, Kong AC, Salaa I, Crouch LI, Ansbro MR, Isaacson SC, Singh H, Barrera NP, Nair AV, Robinson CV, Deery MJ, van Veen HW. Drug-dependent inhibition of nucleotide hydrolysis in the heterodimeric ABC multidrug transporter PatAB from Streptococcus pneumoniae. FEBS J 2022; 289:3770-3788. [PMID: 35066976 PMCID: PMC9541285 DOI: 10.1111/febs.16366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 02/02/2023]
Abstract
The bacterial heterodimeric ATP‐binding cassette (ABC) multidrug exporter PatAB has a critical role in conferring antibiotic resistance in multidrug‐resistant infections by Streptococcus pneumoniae. As with other heterodimeric ABC exporters, PatAB contains two transmembrane domains that form a drug translocation pathway for efflux and two nucleotide‐binding domains that bind ATP, one of which is hydrolysed during transport. The structural and functional elements in heterodimeric ABC multidrug exporters that determine interactions with drugs and couple drug binding to nucleotide hydrolysis are not fully understood. Here, we used mass spectrometry techniques to determine the subunit stoichiometry in PatAB in our lactococcal expression system and investigate locations of drug binding using the fluorescent drug‐mimetic azido‐ethidium. Surprisingly, our analyses of azido‐ethidium‐labelled PatAB peptides point to ethidium binding in the PatA nucleotide‐binding domain, with the azido moiety crosslinked to residue Q521 in the H‐like loop of the degenerate nucleotide‐binding site. Investigation into this compound and residue’s role in nucleotide hydrolysis pointed to a reduction in the activity for a Q521A mutant and ethidium‐dependent inhibition in both mutant and wild type. Most transported drugs did not stimulate or inhibit nucleotide hydrolysis of PatAB in detergent solution or lipidic nanodiscs. However, further examples for ethidium‐like inhibition were found with propidium, novobiocin and coumermycin A1, which all inhibit nucleotide hydrolysis by a non‐competitive mechanism. These data cast light on potential mechanisms by which drugs can regulate nucleotide hydrolysis by PatAB, which might involve a novel drug binding site near the nucleotide‐binding domains.
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Affiliation(s)
| | - Pei-Yu Hsieh
- Department of Pharmacology, University of Cambridge, UK
| | - Anam Ali
- Department of Pharmacology, University of Cambridge, UK
| | - Wilma Shi
- Department of Pharmacology, University of Cambridge, UK
| | - Julie Howard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
| | | | - Alex C Kong
- Department of Pharmacology, University of Cambridge, UK
| | - Ihsene Salaa
- Department of Pharmacology, University of Cambridge, UK
| | - Lucy I Crouch
- Department of Pharmacology, University of Cambridge, UK
| | | | | | | | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Asha V Nair
- Department of Pharmacology, University of Cambridge, UK
| | | | - Michael J Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
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26
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Lacabanne D, Wiegand T, Di Cesare M, Orelle C, Ernst M, Jault JM, Meier BH, Böckmann A. Solid-State NMR Reveals Asymmetric ATP Hydrolysis in the Multidrug ABC Transporter BmrA. J Am Chem Soc 2022; 144:12431-12442. [PMID: 35776907 PMCID: PMC9284561 DOI: 10.1021/jacs.2c04287] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
The detailed mechanism
of ATP hydrolysis in ATP-binding cassette
(ABC) transporters is still not fully understood. Here, we employed 31P solid-state NMR to probe the conformational changes and
dynamics during the catalytic cycle by locking the multidrug ABC transporter
BmrA in prehydrolytic, transition, and posthydrolytic states, using
a combination of mutants and ATP analogues. The 31P spectra
reveal that ATP binds strongly in the prehydrolytic state to both
ATP-binding sites as inferred from the analysis of the nonhydrolytic
E504A mutant. In the transition state of wild-type BmrA, the symmetry
of the dimer is broken and only a single site is tightly bound to
ADP:Mg2+:vanadate, while the second site is more ‘open’
allowing exchange with the nucleotides in the solvent. In the posthydrolytic
state, weak binding, as characterized by chemical exchange with free
ADP and by asymmetric 31P–31P two-dimensional
(2D) correlation spectra, is observed for both sites. Revisiting the 13C spectra in light of these findings confirms the conformational
nonequivalence of the two nucleotide-binding sites in the transition
state. Our results show that following ATP binding, the symmetry of
the ATP-binding sites of BmrA is lost in the ATP-hydrolysis step,
but is then recovered in the posthydrolytic ADP-bound state.
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Affiliation(s)
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Margot Di Cesare
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
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27
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Blair JMA, Zeth K, Bavro VN, Sancho-Vaello E. The role of bacterial transport systems in the removal of host antimicrobial peptides in Gram-negative bacteria. FEMS Microbiol Rev 2022; 46:6617596. [PMID: 35749576 PMCID: PMC9629497 DOI: 10.1093/femsre/fuac032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/23/2022] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Antibiotic resistance is a global issue that threatens our progress in healthcare and life expectancy. In recent years, antimicrobial peptides (AMPs) have been considered as promising alternatives to the classic antibiotics. AMPs are potentially superior due to their lower rate of resistance development, since they primarily target the bacterial membrane ('Achilles' heel' of the bacteria). However, bacteria have developed mechanisms of AMP resistance, including the removal of AMPs to the extracellular space by efflux pumps such as the MtrCDE or AcrAB-TolC systems, and the internalization of AMPs to the cytoplasm by the Sap transporter, followed by proteolytic digestion. In this review, we focus on AMP transport as a resistance mechanism compiling all the experimental evidence for the involvement of efflux in AMP resistance in Gram-negative bacteria and combine this information with the analysis of the structures of the efflux systems involved. Finally, we expose some open questions with the aim of arousing the interest of the scientific community towards the AMPs-efflux pumps interactions. All the collected information broadens our understanding of AMP removal by efflux pumps and gives some clues to assist the rational design of AMP-derivatives as inhibitors of the efflux pumps.
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Affiliation(s)
- Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Kornelius Zeth
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Vassiliy N Bavro
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Enea Sancho-Vaello
- Corresponding author. College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom. E-mail:
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28
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Cooper ZS, Rapp JZ, Shoemaker AMD, Anderson RE, Zhong ZP, Deming JW. Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics. Front Microbiol 2022; 13:879116. [PMID: 35733954 PMCID: PMC9207381 DOI: 10.3389/fmicb.2022.879116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter, particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.
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Affiliation(s)
- Zachary S. Cooper
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
- *Correspondence: Zachary S. Cooper, , orcid.org/0000-0001-6515-7971
| | - Josephine Z. Rapp
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Center for Northern Studies (CEN), Université Laval, Québec, QC, Canada
- Institute of Integrative Biology and Systems (IBIS), Université Laval, Québec, QC, Canada
| | - Anna M. D. Shoemaker
- Department of Earth Sciences, Montana State University, Bozeman, MT, United States
| | - Rika E. Anderson
- Department of Biology, Carleton College, Northfield, MN, United States
| | - Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States
- Department of Microbiology, Ohio State University, Columbus, OH, United States
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W. Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
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29
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Beaver K, Gaffney EM, Minteer SD. Understanding metabolic bioelectrocatalysis of the purple bacterium Rhodobacter capsulatus through substrate modulation. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.140291] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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30
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Liu P, Hu S, He Z, Feng C, Dong G, An S, Liu R, Xu F, Chen Y, Ying X. Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome. Front Microbiol 2022; 13:828254. [PMID: 35602026 PMCID: PMC9119422 DOI: 10.3389/fmicb.2022.828254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Intestinal bacteria strains play crucial roles in maintaining host health. Researchers have increasingly recognized the importance of strain-level analysis in metagenomic studies. Many analysis tools and several cutting-edge sequencing techniques like single cell sequencing have been proposed to decipher strains in metagenomes. However, strain-level complexity is far from being well characterized up to date. As the indicator of strain-level complexity, metagenomic single-nucleotide polymorphisms (SNPs) have been utilized to disentangle conspecific strains. Lots of SNP-based tools have been developed to identify strains in metagenomes. However, the sufficient sequencing depth for SNP and strain-level analysis remains unclear. We conducted ultra-deep sequencing of the human gut microbiome and constructed an unbiased framework to perform reliable SNP analysis. SNP profiles of the human gut metagenome by ultra-deep sequencing were obtained. SNPs identified from conventional and ultra-deep sequencing data were thoroughly compared and the relationship between SNP identification and sequencing depth were investigated. The results show that the commonly used shallow-depth sequencing is incapable to support a systematic metagenomic SNP discovery. In contrast, ultra-deep sequencing could detect more functionally important SNPs, which leads to reliable downstream analyses and novel discoveries. We also constructed a machine learning model to provide guidance for researchers to determine the optimal sequencing depth for their projects (SNPsnp, https://github.com/labomics/SNPsnp). To conclude, the SNP profiles based on ultra-deep sequencing data extend current knowledge on metagenomics and highlights the importance of evaluating sequencing depth before starting SNP analysis. This study provides new ideas and references for future strain-level investigations.
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Affiliation(s)
- Pu Liu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Shuofeng Hu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Zhen He
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Chao Feng
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Guohua Dong
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Sijing An
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Runyan Liu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Fang Xu
- Yongkang First People’s Hospital, Yongkang, China
| | - Yaowen Chen
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xiaomin Ying
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
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31
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Morris DE, Osman KL, Cleary DW, Clarke SC. The characterization of Moraxella catarrhalis carried in the general population. Microb Genom 2022; 8:mgen000820. [PMID: 35639578 PMCID: PMC9465073 DOI: 10.1099/mgen.0.000820] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/30/2022] [Indexed: 12/03/2022] Open
Abstract
Moraxella catarrhalis is a common cause of respiratory tract infection, particularly otitis media in children, whilst it is also associated with the onset of exacerbation in chronic obstructive pulmonary disease in adults. Despite the need for an efficacious vaccine against M. catarrhalis, no candidates have progressed to clinical trial. This study, therefore, aimed to characterize the diversity of M. catarrhalis isolated from the upper respiratory tract of healthy children and adults, to gain a better understanding of the epidemiology of M. catarrhalis and the distribution of genes associated with virulence factors, to aid vaccine efforts. Isolates were sequenced and the presence of target genes reported. Contrary to prevailing data, this study found that lipooligosaccharide (LOS) B serotypes are not exclusively associated with 16S type 1. In addition, a particularly low prevalence of LOS B and high prevalence of LOS C serotypes was observed. M. catarrhalis isolates showed low prevalence of antimicrobial resistance and a high gene prevalence for a number of the target genes investigated: ompB2 (also known as copB), ompCD, ompE, ompG1a, ompG1b, mid (also known as hag), mcaP, m35, tbpA, lbpA, tbpB, lbpB, msp22, msp75 and msp78, afeA, pilA, pilQ, pilT, mod, oppA, sbp2, mcmA and mclS.
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Affiliation(s)
- Denise E. Morris
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Karen L. Osman
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - David W. Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Global Health Research Institute, University of Southampton, Southampton SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton SO16 6YD, UK
| | - Stuart C. Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Global Health Research Institute, University of Southampton, Southampton SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton SO16 6YD, UK
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32
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Iron Reduction in Dermacentor andersoni Tick Cells Inhibits Anaplasma marginale Replication. Int J Mol Sci 2022; 23:ijms23073941. [PMID: 35409307 PMCID: PMC8999750 DOI: 10.3390/ijms23073941] [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: 02/16/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 02/04/2023] Open
Abstract
Anaplasma spp. are obligate intracellular, tick-borne, bacterial pathogens that cause bovine and human anaplasmosis. We lack tools to prevent these diseases in part due to major knowledge gaps in our fundamental understanding of the tick-pathogen interface, including the requirement for and molecules involved in iron transport during tick colonization. We determine that iron is required for the pathogen Anaplasma marginale, which causes bovine anaplasmosis, to replicate in Dermacentor andersoni tick cells. Using bioinformatics and protein modeling, we identified three orthologs of the Gram-negative siderophore-independent iron uptake system, FbpABC. Am069, the A. marginale ortholog of FbpA, lacks predicted iron-binding residues according to the NCBI conserved domain database. However, according to protein modeling, the best structural orthologs of Am069 are iron transport proteins from Cyanobacteria and Campylobacterjejuni. We then determined that all three A. marginale genes are modestly differentially expressed in response to altered host cell iron levels, despite the lack of a Ferric uptake regulator or operon structure. This work is foundational for building a mechanistic understanding of iron uptake, which could lead to interventions to prevent bovine and human anaplasmosis.
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33
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Blanco-Vázquez C, Alonso-Hearn M, Iglesias N, Vázquez P, Juste RA, Garrido JM, Balseiro A, Canive M, Amado J, Queipo MA, Iglesias T, Casais R. Use of ATP-Binding Cassette Subfamily A Member 13 (ABCA13) for Sensitive Detection of Focal Pathological Forms of Subclinical Bovine Paratuberculosis. Front Vet Sci 2022; 9:816135. [PMID: 35359676 PMCID: PMC8960928 DOI: 10.3389/fvets.2022.816135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/24/2022] [Indexed: 12/20/2022] Open
Abstract
Bovine paratuberculosis (PTB) is a chronic enteritis caused by Mycobacterium avium subspecies paratuberculosis (Map) that causes a heavy economic impact worldwide. Map infected animals can remain asymptomatic for years while transmitting the mycobacteria to other members of the herd. Therefore, accurate detection of subclinically infected animals is crucial for disease control. In a previous RNA-Seq study, we identified several mRNAs that were overexpressed in whole blood of cows with different PTB-associated histological lesions compared with control animals without detected lesions. The proteins encoded by two of these mRNAs, ATP binding cassette subfamily A member 13 (ABCA13) and Matrix Metallopeptidase 8 (MMP8) were significantly overexpressed in whole blood of animals with focal histological lesions, the most frequent pathological form in the subclinical stages of the disease. In the current study, the potential of sensitive early diagnostic tools of commercial ELISAs, based on the detection of these two biomarkers, was evaluated in serum samples of 704 Holstein Friesian cows (566 infected animals and 138 control animals from PTB-free farms). For this evaluation, infected animals were classified into three groups, according to the type of histological lesions present in their gut tissues: focal (n = 447), multifocal (n = 59), and diffuse (n = 60). The ELISA based on the detection of ABCA13 was successfully validated showing good discriminatory power between animals with focal lesions and control animals (sensitivity 82.99% and specificity 80.43%). Conversely, the MMP8-based ELISA showed a poor discriminatory power between the different histological groups and non-infected controls. The ABCA13-based ELISA showed a higher diagnostic value (0.822) than the IDEXX ELISA (0.517), the fecal bacterial isolation (0.523) and the real-time PCR (0.531) for the detection of animals with focal lesions. Overall, our results indicate that this ABCA13 ELISA greatly improves the identification of subclinically infected animals with focal lesions that are undetectable using current diagnostic methods.
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Affiliation(s)
- Cristina Blanco-Vázquez
- Centro de Biotecnología Animal, Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Deva, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Natalia Iglesias
- Centro de Biotecnología Animal, Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Deva, Spain
| | - Patricia Vázquez
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Ramón A. Juste
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Joseba M. Garrido
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Ana Balseiro
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
- Instituto de Ganadería de Montaña, Centro Superior de Investigaciones Científicas (CSIC-Universidad de León), León, Spain
| | - María Canive
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Javier Amado
- Laboratorio Regional de Sanidad Animal del Principado de Asturias, Gijón, Spain
| | - Manuel A. Queipo
- Servicio de Sanidad y Producción Animal del Principado de Asturias, Oviedo, Spain
| | - Tania Iglesias
- Unidad de Consultoría Estadística, Servicios científico-técnicos, Universidad de Oviedo, Gijón, Spain
| | - Rosa Casais
- Centro de Biotecnología Animal, Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Deva, Spain
- *Correspondence: Rosa Casais
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34
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Guo Q, Atkinson SD, Xiao B, Zhai Y, Bartholomew JL, Gu Z. A myxozoan genome reveals mosaic evolution in a parasitic cnidarian. BMC Biol 2022; 20:51. [PMID: 35177085 PMCID: PMC8855578 DOI: 10.1186/s12915-022-01249-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/07/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Parasite evolution has been conceptualized as a process of genetic loss and simplification. Contrary to this model, there is evidence of expansion and conservation of gene families related to essential functions of parasitism in some parasite genomes, reminiscent of widespread mosaic evolution-where subregions of a genome have different rates of evolutionary change. We found evidence of mosaic genome evolution in the cnidarian Myxobolus honghuensis, a myxozoan parasite of fish, with extremely simple morphology. RESULTS We compared M. honghuensis with other myxozoans and free-living cnidarians, and determined that it has a relatively larger myxozoan genome (206 Mb), which is less reduced and less compact due to gene retention, large introns, transposon insertion, but not polyploidy. Relative to other metazoans, the M. honghuensis genome is depleted of neural genes and has only the simplest animal immune components. Conversely, it has relatively more genes involved in stress resistance, tissue invasion, energy metabolism, and cellular processes compared to other myxozoans and free-living cnidarians. We postulate that the expansion of these gene families is the result of evolutionary adaptations to endoparasitism. M. honghuensis retains genes found in free-living Cnidaria, including a reduced nervous system, myogenic components, ANTP class Homeobox genes, and components of the Wnt and Hedgehog pathways. CONCLUSIONS Our analyses suggest that the M. honghuensis genome evolved as a mosaic of conservative, divergent, depleted, and enhanced genes and pathways. These findings illustrate that myxozoans are not as genetically simple as previously regarded, and the evolution of some myxozoans is driven by both genomic streamlining and expansion.
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Affiliation(s)
- Qingxiang Guo
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China
| | - Stephen D Atkinson
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Bin Xiao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China
| | - Yanhua Zhai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China
| | - Jerri L Bartholomew
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Zemao Gu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan, 430070, People's Republic of China.
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35
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Guo Z, Gao S, Ding J, He J, Ma L, Bu D. Effects of Heat Stress on the Ruminal Epithelial Barrier of Dairy Cows Revealed by Micromorphological Observation and Transcriptomic Analysis. Front Genet 2022; 12:768209. [PMID: 35096001 PMCID: PMC8793686 DOI: 10.3389/fgene.2021.768209] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/07/2021] [Indexed: 12/30/2022] Open
Abstract
Heat stress (HS) alters the rumen fermentation of dairy cows thereby affecting the metabolism of rumen papillae and thus the epithelial barrier function. The aim of the present study was to investigate if HS damages the barrier function of ruminal epithelia. Eight multiparous Holstein dairy cows with rumen cannula were randomly equally allocated to two replicates (n = 4), with each replicate being subjected to heat stress or thermal neutrality and pair-feeding in four environmental chambers. Micromorphological observation showed HS aggravated the shedding of the corneum and destroyed the physical barrier of the ruminal epithelium to a certain extent. Transcriptomics analysis of the rumen papillae revealed pathways associated with DNA replication and repair and amino acid metabolism were perturbated, the biological processes including sister chromatid segregation, etc. were up-regulated by HS, while the MAPK and NF-kB cell signaling pathways were downregulated. However, no heat stress-specific change in the expression of tight junction protein or TLR4 signaling was found, suggesting that HS negatively affected the physical barrier of the ruminal epithelium to some extent but did not break the ruminal epithelium. Heat stress invoked mechanisms to maintain the integrity of the rumen epithelial barrier by upregulating the expression of heat shock protein and repairments in rumen papillae. The increase in amino acid metabolism in rumen papillae might affect the nutrient utilization of the whole body. The findings of this study may inform future research to better understand how heat stress affects the physiology and productivity of lactating cows and the development of mitigation strategies.
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Affiliation(s)
- Zitai Guo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengtao Gao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Ding
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junhao He
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lu Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Alcorlo M, Martínez-Caballero S, Molina R, Hermoso JA. Regulation of Lytic Machineries by the FtsEX Complex in the Bacterial Divisome. Subcell Biochem 2022; 99:285-315. [PMID: 36151380 DOI: 10.1007/978-3-031-00793-4_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The essential membrane complex FtsE/FtsX (FtsEX), belonging to the ABC transporter superfamily and widespread among bacteria, plays a relevant function in some crucial cell wall remodeling processes such as cell division, elongation, or sporulation. FtsEX plays a double role by recruiting proteins to the divisome apparatus and by regulating lytic activity of the cell wall hydrolases required for daughter cell separation. Interestingly, FtsEX does not act as a transporter but uses the ATPase activity of FtsE to mechanically transmit a signal from the cytosol, through the membrane, to the periplasm that activates the attached hydrolases. While the complete molecular details of such mechanism are not yet known, evidence has been recently reported that clarify essential aspects of this complex system. In this chapter we will present recent structural advances on this topic. The three-dimensional structure of FtsE, FtsX, and some of the lytic enzymes or their cognate regulators revealed an unexpected scenario in which a delicate set of intermolecular interactions, conserved among different bacterial genera, could be at the core of this regulatory mechanism providing exquisite control in both space and time of this central process to assist bacterial survival.
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Affiliation(s)
- Martín Alcorlo
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, Madrid, Spain
| | - Siseth Martínez-Caballero
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, Madrid, Spain
- Department of Chemistry of Biomacromolecules, Universidade Nacional Autonoma de Mexico, Ciudad de México, Mexico
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, Madrid, Spain.
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Brindangnanam P, Sawant AR, Prashanth K, Coumar MS. Bacterial effluxome as a barrier against antimicrobial agents: structural biology aspects and drug targeting. Tissue Barriers 2021; 10:2013695. [PMID: 34957912 DOI: 10.1080/21688370.2021.2013695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is fast becoming a medical crisis affecting the entire global population. The bacterial membrane is the first layer of defense for the bacteria against antimicrobial agents (AMA), specifically transporters in the membrane efflux these AMA out of the bacteria and plays a significant role in the AMR development. Understanding the structure and the functions of these efflux transporters is essential to overcome AMR. This review discusses efflux transporters (primary, secondary, and tripartite), their domain architectures, substrate specificities, and efflux pump inhibitors (EPI). Special emphasis on nosocomial ESKAPEE (Enterococcus faecium., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli) pathogens, their multidrug efflux targets and inhibitors are discussed. Deep knowledge about the functioning of efflux pumps and their structural aspects will open up opportunities for developing new EPI, which could be used along with AMA as combination therapy to overcome the emerging AMR crisis.
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Affiliation(s)
- Pownraj Brindangnanam
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Ajit Ramesh Sawant
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - K Prashanth
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
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Gavas S, Quazi S, Karpiński TM. Nanoparticles for Cancer Therapy: Current Progress and Challenges. NANOSCALE RESEARCH LETTERS 2021; 16:173. [PMID: 34866166 PMCID: PMC8645667 DOI: 10.1186/s11671-021-03628-6] [Citation(s) in RCA: 264] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/19/2021] [Indexed: 05/04/2023]
Abstract
Cancer is one of the leading causes of death and morbidity with a complex pathophysiology. Traditional cancer therapies include chemotherapy, radiation therapy, targeted therapy, and immunotherapy. However, limitations such as lack of specificity, cytotoxicity, and multi-drug resistance pose a substantial challenge for favorable cancer treatment. The advent of nanotechnology has revolutionized the arena of cancer diagnosis and treatment. Nanoparticles (1-100 nm) can be used to treat cancer due to their specific advantages such as biocompatibility, reduced toxicity, more excellent stability, enhanced permeability and retention effect, and precise targeting. Nanoparticles are classified into several main categories. The nanoparticle drug delivery system is particular and utilizes tumor and tumor environment characteristics. Nanoparticles not only solve the limitations of conventional cancer treatment but also overcome multidrug resistance. Additionally, as new multidrug resistance mechanisms are unraveled and studied, nanoparticles are being investigated more vigorously. Various therapeutic implications of nanoformulations have created brand new perspectives for cancer treatment. However, most of the research is limited to in vivo and in vitro studies, and the number of approved nanodrugs has not much amplified over the years. This review discusses numerous types of nanoparticles, targeting mechanisms, and approved nanotherapeutics for oncological implications in cancer treatment. Further, we also summarize the current perspective, advantages, and challenges in clinical translation.
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Affiliation(s)
- Shreelaxmi Gavas
- Department of Life Sciences, GenLab Biosolutions Private Limited, Bangalore, Karnataka 560043 India
| | - Sameer Quazi
- GenLab Biosolutions Private Limited, Bangalore, Karnataka 560043 India
| | - Tomasz M. Karpiński
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Wieniawskiego 3, 61-712 Poznań, Poland
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Viehweger A, Blumenscheit C, Lippmann N, Wyres KL, Brandt C, Hans JB, Hölzer M, Irber L, Gatermann S, Lübbert C, Pletz MW, Holt KE, König B. Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae. Microb Genom 2021; 7:000741. [PMID: 34913861 PMCID: PMC8767333 DOI: 10.1099/mgen.0.000741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/04/2021] [Indexed: 01/18/2023] Open
Abstract
Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done. We investigate two large hospital outbreaks of a carbapenemase-carrying Klebsiella pneumoniae strain in Germany and show the value of contextual data. By screening about 10 000 genomes, over 400 000 metagenomes and two culture collections using in silico and in vitro methods, we identify a total of 415 closely related genomes reported in 28 studies. We identify the relationship between the two outbreaks through time-dated phylogeny, including their respective origin. One of the outbreaks presents extensive hidden transmission, with descendant isolates only identified in other studies. We then leverage the genome collection from this meta-analysis to identify genes under positive selection. We thereby identify an inner membrane transporter (ynjC) with a putative role in colistin resistance. Contextual data from other sources can thus enhance local genomic surveillance at multiple levels and should be integrated by default when available.
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Affiliation(s)
- Adrian Viehweger
- Institute of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany
| | | | - Norman Lippmann
- Institute of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany
| | - Kelly L. Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Christian Brandt
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Jörg B. Hans
- National Reference Center for multidrug-resistant Gram-negative bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Martin Hölzer
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Luiz Irber
- Department of Population Health and Reproduction, University of California, Davis, Davis, California, USA
| | - Sören Gatermann
- National Reference Center for multidrug-resistant Gram-negative bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | - Christoph Lübbert
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine II, University Hospital Leipzig, Leipzig, Germany
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Brigitte König
- Institute of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany
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Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
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Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
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41
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Shim H, Shivram H, Lei S, Doudna JA, Banfield JF. Diverse ATPase Proteins in Mobilomes Constitute a Large Potential Sink for Prokaryotic Host ATP. Front Microbiol 2021; 12:691847. [PMID: 34305853 PMCID: PMC8297831 DOI: 10.3389/fmicb.2021.691847] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
Prokaryote mobilome genomes rely on host machineries for survival and replication. Given that mobile genetic elements (MGEs) derive their energy from host cells, we investigated the diversity of ATP-utilizing proteins in MGE genomes to determine whether they might be associated with proteins that could suppress related host proteins that consume energy. A comprehensive search of 353 huge phage genomes revealed that up to 9% of the proteins have ATPase domains. For example, ATPase proteins constitute ∼3% of the genomes of Lak phages with ∼550 kbp genomes that occur in the microbiomes of humans and other animals. Statistical analysis shows the number of ATPase proteins increases linearly with genome length, consistent with a large sink for host ATP during replication of megaphages. Using metagenomic data from diverse environments, we found 505 mobilome proteins with ATPase domains fused to diverse functional domains. Among these composite ATPase proteins, 61.6% have known functional domains that could contribute to host energy diversion during the mobilome infection cycle. As many have domains that are known to interact with nucleic acids and proteins, we infer that numerous ATPase proteins are used during replication and for protection from host immune systems. We found a set of uncharacterized ATPase proteins with nuclease and protease activities, displaying unique domain architectures that are energy intensive based on the presence of multiple ATPase domains. In many cases, these composite ATPase proteins genomically co-localize with small proteins in genomic contexts that are reminiscent of toxin-antitoxin systems and phage helicase-antibacterial helicase systems. Small proteins that function as inhibitors may be a common strategy for control of cellular processes, thus could inspire future biochemical experiments for the development of new nucleic acid and protein manipulation tools, with diverse biotechnological applications.
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Affiliation(s)
- Hyunjin Shim
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | - Haridha Shivram
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Shufei Lei
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, United States.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Chan Zuckerberg Biohub, San Francisco, CA, United States.,School of Earth Sciences, University of Melbourne, Melbourne, VIC, Australia
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42
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Xie X, Cao P, Wang Z, Gao J, Wu M, Li X, Zhang J, Wang Y, Gong D, Yang J. Genome-wide characterization and expression profiling of the PDR gene family in tobacco (Nicotiana tabacum). Gene 2021; 788:145637. [PMID: 33848571 DOI: 10.1016/j.gene.2021.145637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/13/2021] [Accepted: 04/07/2021] [Indexed: 11/18/2022]
Abstract
The pleiotropic drug resistance (PDR) proteins of the ATP-binding cassette (ABC) family play essential roles in physiological processes and have been characterized in many plant species. However, no comprehensive investigation of tobacco (Nicotiana tabacum), an important economic crop and a useful model plant for scientific research, has been presented. We identified 32 PDR genes in the tobacco genome and explored their domain organization, chromosomal distribution and evolution, promoter cis-elements, and expression profiles. A phylogenetic analysis revealed that tobacco has a significantly expanded number of PDR genes involved in plant defense. It also revealed that two tobacco PDR proteins may function as strigolactone transporters to regulate shoot branching, and several NtPDR genes may be involved in cadmium transport. Moreover, tissue expression profiles of NtPDR genes and their responses to several hormones and abiotic stresses were assessed using quantitative real-time PCR. Most of the NtPDR genes were regulated by jasmonate or salicylic acid, suggesting the important regulatory roles of NtPDRs in plant defense and secondary metabolism. They were also responsive to abiotic stresses, like drought and cold, and there was a strong correlation between the presence of promoter cis-elements and abiotic/biotic stress responses. These results provide useful clues for further in-depth studies on the functions of the tobacco PDR genes.
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Affiliation(s)
- Xiaodong Xie
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Zhong Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Junping Gao
- China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Mingzhu Wu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Xiaoxu Li
- China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Jianfeng Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Yaofu Wang
- China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China
| | - Daping Gong
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China.
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China.
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Zhou C, Shi H, Zhang M, Zhou L, Xiao L, Feng S, Im W, Zhou M, Zhang X, Huang Y. Structural Insight into Phospholipid Transport by the MlaFEBD Complex from P. aeruginosa. J Mol Biol 2021; 433:166986. [PMID: 33845086 DOI: 10.1016/j.jmb.2021.166986] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 11/27/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria, which consists of lipopolysaccharides (LPS) in the outer leaflet and phospholipids (PLs) in the inner leaflet, plays a key role in antibiotic resistance and pathogen virulence. The maintenance of lipid asymmetry (Mla) pathway is known to be involved in PL transport and contributes to the lipid homeostasis of the OM, yet the underlying molecular mechanism and the directionality of PL transport in this pathway remain elusive. Here, we reported the cryo-EM structures of the ATP-binding cassette (ABC) transporter MlaFEBD from P. areuginosa, the core complex in the Mla pathway, in nucleotide-free (apo)-, ADP (ATP + vanadate)- and ATP (AMPPNP)-bound states as well as the structures of MlaFEB from E. coli in apo- and AMPPNP-bound states at a resolution range of 3.4-3.9 Å. The structures show that the MlaFEBD complex contains a total of twelve protein molecules with a stoichiometry of MlaF2E2B2D6, and binds a plethora of PLs at different locations. In contrast to canonical ABC transporters, nucleotide binding fails to trigger significant conformational changes of both MlaFEBD and MlaFEB in the nucleotide-binding and transmembrane domains of the ABC transporter, correlated with their low ATPase activities exhibited in both detergent micelles and lipid nanodiscs. Intriguingly, PLs or detergents appeared to relocate to the membrane-proximal end from the distal end of the hydrophobic tunnel formed by the MlaD hexamer in MlaFEBD upon addition of ATP, indicating that retrograde PL transport might occur in the tunnel in an ATP-dependent manner. Site-specific photocrosslinking experiment confirms that the substrate-binding pocket in the dimeric MlaE and the MlaD hexamer are able to bind PLs in vitro, in line with the notion that MlaFEBD complex functions as a PL transporter.
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Affiliation(s)
- Changping Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing100101, China
| | - Huigang Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing100101, China
| | - Manfeng Zhang
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lijun Zhou
- Institute of Bio-analytical Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiao Ling Wei Street, Nanjing 210094, China
| | - Le Xiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing100101, China
| | - Shasha Feng
- Departments of Biological Sciences and Chemistry, Lehigh University, PA 18015, USA
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, PA 18015, USA
| | - Min Zhou
- Institute of Bio-analytical Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiao Ling Wei Street, Nanjing 210094, China.
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing100101, China.
| | - Yihua Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing100101, China.
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44
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Cardiolipin aids in lipopolysaccharide transport to the gram-negative outer membrane. Proc Natl Acad Sci U S A 2021; 118:2018329118. [PMID: 33833055 DOI: 10.1073/pnas.2018329118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In Escherichia coli, cardiolipin (CL) is the least abundant of the three major glycerophospholipids in the gram-negative cell envelope. However, E. coli harbors three distinct enzymes that synthesize CL: ClsA, ClsB, and ClsC. This redundancy suggests that CL is essential for bacterial fitness, yet CL-deficient bacteria are viable. Although multiple CL-protein interactions have been identified, the role of CL still remains unclear. To identify genes that impact fitness in the absence of CL, we analyzed high-density transposon (Tn) mutant libraries in combinatorial CL synthase mutant backgrounds. We found LpxM, which is the last enzyme in lipid A biosynthesis, the membrane anchor of lipopolysaccharide (LPS), to be critical for viability in the absence of clsA Here, we demonstrate that CL produced by ClsA enhances LPS transport. Suppressors of clsA and lpxM essentiality were identified in msbA, a gene that encodes the indispensable LPS ABC transporter. Depletion of ClsA in ∆lpxM mutants increased accumulation of LPS in the inner membrane, demonstrating that the synthetic lethal phenotype arises from improper LPS transport. Additionally, overexpression of ClsA alleviated ΔlpxM defects associated with impaired outer membrane asymmetry. Mutations that lower LPS levels, such as a YejM truncation or alteration in the fatty acid pool, were sufficient in overcoming the synthetically lethal ΔclsA ΔlpxM phenotype. Our results support a model in which CL aids in the transportation of LPS, a unique glycolipid, and adds to the growing repertoire of CL-protein interactions important for bacterial transport systems.
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Król-Górniak A, Pomastowski P, Railean-Plugaru V, Žuvela P, Wong MW, Pauter K, Szultka-Młyńska M, Buszewski B. The study of the molecular mechanism of Lactobacillus paracasei clumping via divalent metal ions by electrophoretic separation. J Chromatogr A 2021; 1652:462127. [PMID: 34214833 DOI: 10.1016/j.chroma.2021.462127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 11/18/2022]
Abstract
In this work, the molecular mechanism of Lactobacillus paracasei bio-colloid clumping under divalent metal ions treatment such as zinc, copper and magnesium at constant concentrations was studied. The work involved experimental (electrophoretic - capillary electrophoresis in pseudo-isotachophoresis mode, spectroscopic and spectrometric - FT-IR and MALDI-TOF-MS, microscopic - fluorescent microscopy, and flow cytometry) and theoretical (DFT calculations of model complex systems) characterization. Electrophoretic results have pointed out the formation of aggregates under the Zn2+ and Cu2+ modification, whereas the use of the Mg2+ allowed focusing the zone of L. paracasei biocolloid. According to the FT-IR analysis, the major functional groups involved in the aggregation are deprotonated carboxyl and amide groups derived from the bacterial surface structure. Nature of the divalent metal ions was shown to be one of the key factors influencing the bacterial aggregation process. Proteomic analysis showed that surface modification had a considerable impact on bacteria molecular profiles and protein expression, mainly linked to the activation of carbohydrate and nucleotides metabolism as well with the transcription regulation and membrane transport. Density-functional theory (DFT) calculations of modeled Cu2+, Mg2+ and Zn2+ coordination complexes support the interaction between the divalent metal ions and bacterial proteins. Consequently, the possible mechanism of the aggregation phenomenon was proposed. Therefore, this comprehensive study could be further applied in evaluation of biocolloid aggregation under different types of metal ions.
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Affiliation(s)
- Anna Król-Górniak
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 7 Gagarina Str., 87-100 Torun, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 7 Gagarina Str., 87-100 Torun, Poland
| | - Viorica Railean-Plugaru
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 7 Gagarina Str., 87-100 Torun, Poland
| | - Petar Žuvela
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Katarzyna Pauter
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 7 Gagarina Str., 87-100 Torun, Poland
| | - Małgorzata Szultka-Młyńska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 7 Gagarina Str., 87-100 Torun, Poland
| | - Bogusław Buszewski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 7 Gagarina Str., 87-100 Torun, Poland.
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46
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Henderson PJF, Maher C, Elbourne LDH, Eijkelkamp BA, Paulsen IT, Hassan KA. Physiological Functions of Bacterial "Multidrug" Efflux Pumps. Chem Rev 2021; 121:5417-5478. [PMID: 33761243 DOI: 10.1021/acs.chemrev.0c01226] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial multidrug efflux pumps have come to prominence in human and veterinary pathogenesis because they help bacteria protect themselves against the antimicrobials used to overcome their infections. However, it is increasingly realized that many, probably most, such pumps have physiological roles that are distinct from protection of bacteria against antimicrobials administered by humans. Here we undertake a broad survey of the proteins involved, allied to detailed examples of their evolution, energetics, structures, chemical recognition, and molecular mechanisms, together with the experimental strategies that enable rapid and economical progress in understanding their true physiological roles. Once these roles are established, the knowledge can be harnessed to design more effective drugs, improve existing microbial production of drugs for clinical practice and of feedstocks for commercial exploitation, and even develop more sustainable biological processes that avoid, for example, utilization of petroleum.
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Affiliation(s)
- Peter J F Henderson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Claire Maher
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Liam D H Elbourne
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Ian T Paulsen
- Department of Biomolecular Sciences, Macquarie University, Sydney 2109, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
| | - Karl A Hassan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan 2308, New South Wales, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney 2019, New South Wales, Australia
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47
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Yang CC, Yokoi K, Yamamoto K, Jouraku A. An update of KAIKObase, the silkworm genome database. Database (Oxford) 2021; 2021:baaa099. [PMID: 33645624 PMCID: PMC7918157 DOI: 10.1093/database/baaa099] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022]
Abstract
KAIKObase was established in 2009 as the genome database of the domesticated silkworm Bombyx mori. It provides several gene sets and genetic maps as well as genome annotation obtained from the sequencing project of the International Silkworm Genome Consortium in 2008. KAIKObase has been used widely for silkworm and insect studies even though there are some erroneous predicted genes due to misassembly and gaps in the genome. In 2019, we released a new silkworm genome assembly, showing improvements in gap closure and covering more and longer gene models. Therefore, there is a need to include new genome and new gene models to KAIKObase. In this article, we present the updated contents of KAIKObase and the methods to generate, integrate and analyze the data sets. Database URL: https://kaikobase.dna.affrc.go.jp.
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Affiliation(s)
- Ching-chia Yang
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Kakeru Yokoi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Kimiko Yamamoto
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Akiya Jouraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
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48
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Cuajungco MP, Ramirez MS, Tolmasky ME. Zinc: Multidimensional Effects on Living Organisms. Biomedicines 2021; 9:biomedicines9020208. [PMID: 33671781 PMCID: PMC7926802 DOI: 10.3390/biomedicines9020208] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 12/28/2022] Open
Abstract
Zinc is a redox-inert trace element that is second only to iron in abundance in biological systems. In cells, zinc is typically buffered and bound to metalloproteins, but it may also exist in a labile or chelatable (free ion) form. Zinc plays a critical role in prokaryotes and eukaryotes, ranging from structural to catalytic to replication to demise. This review discusses the influential properties of zinc on various mechanisms of bacterial proliferation and synergistic action as an antimicrobial element. We also touch upon the significance of zinc among eukaryotic cells and how it may modulate their survival and death through its inhibitory or modulatory effect on certain receptors, enzymes, and signaling proteins. A brief discussion on zinc chelators is also presented, and chelating agents may be used with or against zinc to affect therapeutics against human diseases. Overall, the multidimensional effects of zinc in cells attest to the growing number of scientific research that reveal the consequential prominence of this remarkable transition metal in human health and disease.
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49
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Niu L, Li H, Song Z, Dong B, Cao H, Liu T, Du T, Yang W, Amin R, Wang L, Yang Q, Meng D, Fu Y. The functional analysis of ABCG transporters in the adaptation of pigeon pea ( Cajanus cajan) to abiotic stresses. PeerJ 2021; 9:e10688. [PMID: 33552725 PMCID: PMC7821757 DOI: 10.7717/peerj.10688] [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] [Received: 10/31/2019] [Accepted: 12/11/2020] [Indexed: 11/21/2022] Open
Abstract
ATP-binding cassette (ABC) transporters are a class of proteins found in living organisms that mediate transmembrane transport by hydrolyzing ATP. They play a vital role in the physiological processes of growth and development in plants. The most numerous sub-type transporter in the ABC transporter family is the ABCG group and which have the most complex function in a plant’s response to abiotic stresses. Our study focused on the effect of ABCG transporters in the adaptation of the pigeon pea to adverse environments (such as drought, salt, temperature, etc.). We conducted a functional analysis of ABCG transporters in the pigeon pea and their role in response to abiotic stresses. A total of 51 ABCG genes (CcABCGs) were identified, and phylogenetic analysis was conducted. We also identified the physicochemical properties of the encoded proteins, predicted their subcellular localization, and identified of the conserved domains. Expression analysis showed that ABCG genes have different expression profiles with tissues and abiotic stresses. Our results showed that CcABCG28 was up-regulated at low temperatures, and CcABCG7 was up-regulated with drought and aluminum stress. The initial results revealed that ABCG transporters are more effective in the abiotic stress resistance of pigeon peas, which improves our understanding of their application in abiotic stress resistance.
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Affiliation(s)
- Lili Niu
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, People's Republic of China
| | - Hanghang Li
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, People's Republic of China
| | - Zhihua Song
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, People's Republic of China
| | - Biying Dong
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, People's Republic of China
| | - Hongyan Cao
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, People's Republic of China
| | - Tengyue Liu
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, People's Republic of China
| | - Tingting Du
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, People's Republic of China
| | - Wanlong Yang
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, People's Republic of China
| | - Rohul Amin
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China
| | - Litao Wang
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China
| | - Qing Yang
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, People's Republic of China
| | - Dong Meng
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, People's Republic of China
| | - Yujie Fu
- The College of Forestry, Beijing Forestry University, Beijing, People's Republic of China.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing, People's Republic of China.,Key Laboratory of Forestry Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, People's Republic of China
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50
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Nuryady MM, Nurcahyo RW, Hindun I, Fatmawati D. Multidrug resistance protein structure of Trypanosoma evansi isolated from buffaloes in Ngawi District, Indonesia: A bioinformatics analysis. Vet World 2021; 14:33-39. [PMID: 33642783 PMCID: PMC7896887 DOI: 10.14202/vetworld.2021.33-39] [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: 07/14/2020] [Accepted: 11/03/2020] [Indexed: 12/05/2022] Open
Abstract
Background and Aim: Trypanosomiasis, also known as surra, is an infectious disease with a wide host spectrum. In Indonesia, this disease is caused by Trypanosoma evansi. Various trypanocidal drugs have been used to treat this pathogen and subsequent disease. Yet, the long-term trypanocidal administration generates drug-resistant T. evansi. Some have identified genetic alterations in T. evansi transporter protein-coding genes that may be responsible for drug resistance. The Multidrug Resistance Protein E (MRPE) gene is a likely candidate gene responsible for the individual resistance. To date, no research has focused on T. evansi MRPE (TevMRPE) in this context. Hence, this research aimed at analyzing and characterizing the TevMRPE gene and protein using a bioinformatics approach. Materials and Methods: T. evansi was isolated from buffalo suffering from surra in Ngawi Regency, Indonesia. Isolated T. evansi was inoculated and cultured in male mice. The T. evansi genome was isolated from mouse blood with a parasitemia degree as high as 105. A polymerase chain reaction procedure was conducted to amplify the putative MRPE coding gene. The amplicon was sequenced and analyzed using MEGA X, BLAST, and I-tasser softwares. Results: The putative TevMRPE coding gene showed sequence similarity as high as 99.79% against the MRPE gene from Trypanosoma brucei gambiense. The protein profile and characteristics depicted that the putative TevMRPE protein was related to a family of Adenosine Triphosphate-Binding Cassette (ABC) transporter proteins. This family of transporter proteins plays a crucial role in the resistance toward several medicines. Conclusion: The obtained gene sequence in this research was identified as the TevMRPE. This gene is homologous to the T. brucei gambiense MRPE gene and possesses ligand active sites for Adenylyl Imidodiphosphate. In addition, MRPE contains enzyme active sites similar to the cystic fibrosis transmembrane conductance regulator. These data suggest that ABC transport proteins, like MRPE, may be necessary to confer trypanocidal drug resistance in T. evansi.
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Affiliation(s)
- Moh Mirza Nuryady
- Department of Biology Education, Faculty of Teacher Training and Education, Universitas Muhammadiyah Malang, Malang, Indonesia.,Master Program of Veterinary Science, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Raden Wisnu Nurcahyo
- Master Program of Veterinary Science, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Department of Parasitology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Iin Hindun
- Department of Biology Education, Faculty of Teacher Training and Education, Universitas Muhammadiyah Malang, Malang, Indonesia
| | - Diani Fatmawati
- Department of Biology Education, Faculty of Teacher Training and Education, Universitas Muhammadiyah Malang, Malang, Indonesia
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