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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [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: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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2
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Rout AK, Tripathy PS, Dixit S, Behera DU, Behera B, Das BK, Behera BK. Unveiling the Microbiome Landscape: A Metagenomic Study of Bacterial Diversity, Antibiotic Resistance, and Virulence Factors in the Sediments of the River Ganga, India. Antibiotics (Basel) 2023; 12:1735. [PMID: 38136769 PMCID: PMC10740832 DOI: 10.3390/antibiotics12121735] [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: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
The global rise in antibiotic resistance, fueled by indiscriminate antibiotic usage in medicine, aquaculture, agriculture, and the food industry, presents a significant public health challenge. Urban wastewater and sewage treatment plants have become key sources of antibiotic resistance proliferation. The present study focuses on the river Ganges in India, which is heavily impacted by human activities and serves as a potential hotspot for the spread of antibiotic resistance. We conducted a metagenomic analysis of sediment samples from six distinct locations along the river to assess the prevalence and diversity of antibiotic resistance genes (ARGs) within the microbial ecosystem. The metagenomic analysis revealed the predominance of Proteobacteria across regions of the river Ganges. The antimicrobial resistance (AMR) genes and virulence factors were determined by various databases. In addition to this, KEGG and COG analysis revealed important pathways related to AMR. The outcomes highlight noticeable regional differences in the prevalence of AMR genes. The findings suggest that enhancing health and sanitation infrastructure could play a crucial role in mitigating the global impact of AMR. This research contributes vital insights into the environmental aspects of antibiotic resistance, highlighting the importance of targeted public health interventions in the fight against AMR.
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Affiliation(s)
- Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR—Central Inland Fisheries Research Institute, Kolkata 700120, WB, India; (A.K.R.); (B.K.D.)
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, OD, India;
| | - Partha Sarathi Tripathy
- Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway;
| | - Sangita Dixit
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to Be University), Bhubaneswar 751030, OD, India; (S.D.); (D.U.B.)
| | - Dibyajyoti Uttameswar Behera
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to Be University), Bhubaneswar 751030, OD, India; (S.D.); (D.U.B.)
| | - Bhaskar Behera
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, OD, India;
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR—Central Inland Fisheries Research Institute, Kolkata 700120, WB, India; (A.K.R.); (B.K.D.)
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR—Central Inland Fisheries Research Institute, Kolkata 700120, WB, India; (A.K.R.); (B.K.D.)
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Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
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Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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Cao K, Wang Y, Bai X, Wang J, Zhang L, Tang Y, Thuku RC, Hou W, Mo G, Chen F, Jin L. Comparison of Fecal Antimicrobial Resistance Genes in Captive and Wild Asian Elephants. Antibiotics (Basel) 2023; 12:antibiotics12050859. [PMID: 37237762 DOI: 10.3390/antibiotics12050859] [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: 03/30/2023] [Revised: 04/22/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The Asian elephant (Elephas maximus) is a flagship species of tropical rainforests, and it has generated much concern. In this case, the gut bacterial communities of captive and wild Asian elephants are particularly noteworthy. We aim to compare the differences in bacterial diversity and antibiotic resistance gene (ARG) subtypes in fecal samples of Asian elephants from different habitats, which may affect host health. Analyses reveal that differences in the dominant species of gut bacteria between captive and wild Asian elephants may result in significant differences in ARGs. Network analysis of bacterial communities in captive Asian elephants has identified potentially pathogenic species. Many negative correlations in network analysis suggest that different food sources may lead to differences in bacterial communities and ARGs. Results also indicate that the ARG levels in local captive breeding of Asian elephants are close to those of the wild type. However, we found that local captive elephants carry fewer ARG types than their wild counterparts. This study reveals the profile and relationship between bacterial communities and ARGs in different sources of Asian elephant feces, providing primary data for captive breeding and rescuing wild Asian elephants.
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Affiliation(s)
- Kaixun Cao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yepeng Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Xuewei Bai
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Jishan Wang
- Asian Elephant Research Center of National Forestry and Grassland Administration, Kunming 650031, China
- Southwest Survey and Planning Institute of National Forestry and Grassland Administration, Kunming 650031, China
| | - Liting Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongjing Tang
- Asian Elephant Research Center of National Forestry and Grassland Administration, Kunming 650031, China
- Southwest Survey and Planning Institute of National Forestry and Grassland Administration, Kunming 650031, China
| | - Rebecca Caroline Thuku
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wei Hou
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Guoxiang Mo
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Chen
- Asian Elephant Research Center of National Forestry and Grassland Administration, Kunming 650031, China
- Southwest Survey and Planning Institute of National Forestry and Grassland Administration, Kunming 650031, China
| | - Lin Jin
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
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LaGree TJ, Byrd BA, Quelle RM, Schofield SL, Mok WWK. Stimulating Transcription in Antibiotic-Tolerant Escherichia coli Sensitizes It to Fluoroquinolone and Nonfluoroquinolone Topoisomerase Inhibitors. Antimicrob Agents Chemother 2023; 67:e0163922. [PMID: 36951560 PMCID: PMC10112259 DOI: 10.1128/aac.01639-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
Antibiotic tolerant bacteria and persistent cells that remain alive after a course of antibiotic treatment can foster the chronicity of infections and the development of antibiotic resistance. Elucidating how bacteria overcome antibiotic action and devising strategies to bolster a new drug's activity can allow us to preserve our antibiotic arsenal. Here, we investigate strategies to potentiate the activities of topoisomerase inhibitors against nongrowing Escherichia coli that are often recalcitrant to existing antibiotics. We focus on sensitizing bacteria to the fluoroquinolone (FQ) levofloxacin (Levo) and to the spiropyrimidinetrione zoliflodacin (Zoli)-the first antibiotic in its class of compounds in clinical development. We found that metabolic stimulation either alone or in combination with inhibiting the AcrAB-TolC efflux pump sensitized stationary-phase E. coli to Levo and Zoli. We demonstrate that the added metabolites increased proton motive force generation and ATP production in stationary-phase cultures without restarting growth. Instead, the stimulated bacteria increased transcription and translation, which rendered the populations more susceptible to topoisomerase inhibitors. Our findings illuminate potential vulnerabilities of antibiotic-tolerant bacteria that can be leveraged to sensitize them to new and existing classes of topoisomerase inhibitors. These approaches enable us to stay one step ahead of adaptive bacteria and safeguard the efficacy of our existing antibiotics.
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Affiliation(s)
- Travis J. LaGree
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Brandon A. Byrd
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
- School of Medicine, University of Connecticut, Farmington, Connecticut, USA
| | - Ryan M. Quelle
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Stephanie L. Schofield
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Wendy W. K. Mok
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, Connecticut, USA
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Browning DF, Hobman JL, Busby SJW. Laboratory strains of Escherichia coli K-12: things are seldom what they seem. Microb Genom 2023; 9:mgen000922. [PMID: 36745549 PMCID: PMC9997739 DOI: 10.1099/mgen.0.000922] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli K-12 was originally isolated 100 years ago and since then it has become an invaluable model organism and a cornerstone of molecular biology research. However, despite its pedigree, since its initial isolation E. coli K-12 has been repeatedly cultured, passaged and mutagenized, resulting in an organism that carries many genetic changes. To understand more about this important model organism, we have sequenced the genomes of two ancestral K-12 strains, WG1 and EMG2, considered to be the progenitors of many key laboratory strains. Our analysis confirms that these strains still carry genetic elements such as bacteriophage lambda (λ) and the F plasmid, but also indicates that they have undergone extensive laboratory-based evolution. Thus, scrutinizing the genomes of ancestral E. coli K-12 strains leads us to examine whether E. coli K-12 is a sufficiently robust model organism for 21st century microbiology.
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Affiliation(s)
- Douglas F Browning
- School of Biosciences, College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK
| | - Stephen J W Busby
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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Yaseen M, Farooq S, Khan A, Shah N, Shah LA, Bibi S, Khan IU, Ahmad S.
CuO‐SiO
2
based nanocomposites: Synthesis, characterization, photocatalytic, antileishmanial, and antioxidant studies. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Muhammad Yaseen
- Department of Chemistry Abdul Wali Khan University Mardan Pakistan
| | - Saima Farooq
- Department of Biological Sciences and Chemistry, College of Arts and Sciences University of Nizwa Nizwa Oman
| | - Abbas Khan
- Department of Chemistry Abdul Wali Khan University Mardan Pakistan
| | - Nasrullah Shah
- Department of Chemistry Abdul Wali Khan University Mardan Pakistan
| | - Luqman Ali Shah
- National Centre of Excellence in Physical Chemistry University of Peshawar Peshawar Pakistan
| | - Shaista Bibi
- Department of Chemistry Abdul Wali Khan University Mardan Pakistan
| | - Imdad Ullah Khan
- Department of Biotechnology Abdul Wali Khan University Mardan Pakistan
| | - Sajjad Ahmad
- Department of Zoology Abdul Wali Khan University Mardan Pakistan
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The Structural and Functional Study of Efflux Pumps Belonging to the RND Transporters Family from Gram-Negative Bacteria. Antibiotics (Basel) 2022; 11:antibiotics11040429. [PMID: 35453181 PMCID: PMC9030541 DOI: 10.3390/antibiotics11040429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 02/01/2023] Open
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