1
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Hong Y, Sun G, Sun S, Miao L, Yang H, Wu B, Ma T, Chen S, Sun L, Yang J, Sun Y, Liu Y, Zang H, Li C. Enhancement of triclocarban biodegradation: Metabolic division of labor in co-culture of Rhodococcus sp. BX2 and Pseudomonas sp. LY-1. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124346. [PMID: 38852663 DOI: 10.1016/j.envpol.2024.124346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Triclocarban (TCC) and its metabolite, 3,4-dichloroaniline (DCA), are classified as emerging organic contaminants (EOCs). Significant concerns arise from water and soil contamination with TCC and its metabolites. These concerns are especially pronounced at high concentrations of up to approximately 20 mg/kg dry weight, as observed in wastewater treatment plants (WWTPs). Here, a TCC-degrading co-culture system comprising Rhodococcus rhodochrous BX2 and Pseudomonas sp. LY-1 was utilized to degrade TCC (14.5 mg/L) by 85.9% in 7 days, showing improved degradation efficiency compared with monocultures. A combination of high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), genome sequencing, transcriptomic analysis, and quantitative reverse transcription-PCR (qRT-PCR) was performed. Meanwhile, through the combination of further experiments involving heterologous expression and gene knockout, we proposed three TCC metabolic pathways and identified four key genes (tccG, tccS, phB, phL) involved in the TCC degradation process. Moreover, we revealed the internal labor division patterns and connections in the co-culture system, indicating that TCC hydrolysis products were exchanged between co-cultured strains. Additionally, mutualistic cooperation between BX2 and LY-1 enhances TCC degradation efficiency. Finally, phytotoxicity assays confirmed a significant reduction in the plant toxicity of TCC following synergistic degradation by two strains. The in-depth understanding of the TCC biotransformation mechanisms and microbial interactions provides useful information for elucidating the mechanism of the collaborative biodegradation of various contaminants.
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Affiliation(s)
- Yaqi Hong
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Guanjun Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Shanshan Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, Department of Bioengineering, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin, 150080, PR China
| | - Lei Miao
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Hua Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Bowen Wu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Tian Ma
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Siyuan Chen
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Liwen Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Jie Yang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yueling Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Yi Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China
| | - Hailian Zang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China; Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, 150030, PR China
| | - Chunyan Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, PR China; Key Laboratory of Swine Facilities Engineering, Ministry of Agriculture and Rural Affairs, Harbin, 150030, PR China.
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2
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Cerna‐Vargas JP, Krell T. Exploring solute binding proteins in Pseudomonas aeruginosa that bind to γ-aminobutyrate and 5-aminovalerate and their role in activating sensor kinases. Microbiologyopen 2024; 13:e1415. [PMID: 38780167 PMCID: PMC11113362 DOI: 10.1002/mbo3.1415] [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: 04/08/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
The standard method of receptor activation involves the binding of signals or signal-loaded solute binding proteins (SBPs) to sensor domains. Many sensor histidine kinases (SHKs), which are activated by SBP binding, are encoded adjacent to their corresponding sbp gene. We examined three SBPs of Pseudomonas aeruginosa PAO1, encoded near the genes for the AgtS (PA0600) and AruS (PA4982) SHKs, to determine how common this arrangement is. Ligand screening and microcalorimetric studies revealed that the SBPs PA0602 and PA4985 preferentially bind to GABA (KD = 2.3 and 0.58 μM, respectively), followed by 5-aminovalerate (KD = 30 and 1.6 μM, respectively) and ethanoldiamine (KD = 2.3 and 0.58 μM, respectively). In contrast, AgtB (PA0604) exclusively recognizes 5-aminovaleric acid (KD = 2.9 μM). However, microcalorimetric titrations did not show any binding between the AgtS sensor domain and AgtB or PA0602, regardless of the presence of ligands. Similarly, bacterial two-hybrid assays did not demonstrate an interaction between PA4985 and the AruS sensor domain. Therefore, sbp and shk genes located nearby are not always functionally linked. We previously identified PA0222 as a GABA-specific SBP. The presence of three SBPs for GABA may be linked to GABA's role as a trigger for P. aeruginosa virulence.
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Affiliation(s)
- Jean Paul Cerna‐Vargas
- Department of Biotechnology and Environmental Protection, Estación Experimental del ZaidínConsejo Superior de Investigaciones CientíficasGranadaSpain
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones CientíficasParque Científico y Tecnológico de la Universidad Politécnica de Madrid, Pozuelo de AlarcónMadridSpain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del ZaidínConsejo Superior de Investigaciones CientíficasGranadaSpain
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3
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Zhao Z, Ling Z, Nie X, Liu D, Chen H, Zhang S. Microbial Diversity and Community Structure of Chinese Fresh Beef during Cold Storage and Their Correlations with Off-Flavors. Foods 2024; 13:1482. [PMID: 38790782 PMCID: PMC11119422 DOI: 10.3390/foods13101482] [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: 03/24/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
To investigate the diversity and dynamics of microorganisms in Chinese fresh beef (CFB) without acid discharge treatment during cold storage, high-throughput sequencing was employed to analyze the CFB refrigerated for 0, 3, 7, and 10 days. The results showed that the community richness of the fungi and bacteria decreased significantly. However, the diversity decreased in the early stage and increased in the later stage. At the phylum level, Ascomycota (74.1-94.1%) and Firmicutes (77.3-96.8%) were the absolutely dominant fungal and bacterial phyla. The relative abundance of both fungal and bacterial phyla displayed a trend of increasing and then decreasing. At the genus level, Candida (29.3-52.5%) and Lactococcus (19.8-59.3%) were, respectively, the dominant fungal and bacterial genera. The relative abundance of Candida showed a trend of increasing and then decreasing, while Lactococcus possessed the opposite trend. KEGG metabolic pathways analysis suggested that carbohydrate metabolism, membrane transport, and amino acid metabolism were the major metabolic pathways of bacteria. Bugbase prediction indicated the major microbial phenotype of bacteria in CFB during cold storage was Gram-positive (17.2-31.6%). Correlation analysis suggested that Lactococcus, Citrobacter, Proteus, and Rhodotorula might be the main microorganisms promoting the production of off-flavor substances in CFB. This study provides a theoretical basis for the preservation of Chinese fresh beef.
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Affiliation(s)
- Zhiping Zhao
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Z.Z.); (Z.L.); (H.C.); (S.Z.)
| | - Ziqing Ling
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Z.Z.); (Z.L.); (H.C.); (S.Z.)
- College of Food Science and Technology, Sichuan Tourism University, Chengdu 610100, China;
| | - Xin Nie
- College of Food Science and Technology, Sichuan Tourism University, Chengdu 610100, China;
| | - Dayu Liu
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Z.Z.); (Z.L.); (H.C.); (S.Z.)
| | - Hongfan Chen
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Z.Z.); (Z.L.); (H.C.); (S.Z.)
- College of Food Science and Technology, Sichuan Tourism University, Chengdu 610100, China;
| | - Shengyuan Zhang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Z.Z.); (Z.L.); (H.C.); (S.Z.)
- College of Food Science and Technology, Sichuan Tourism University, Chengdu 610100, China;
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4
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Kion-Crosby W, Barquist L. Network depth affects inference of gene sets from bacterial transcriptomes using denoising autoencoders. BIOINFORMATICS ADVANCES 2024; 4:vbae066. [PMID: 39027639 PMCID: PMC11256956 DOI: 10.1093/bioadv/vbae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/05/2024] [Accepted: 05/02/2024] [Indexed: 07/20/2024]
Abstract
Summary The increasing number of publicly available bacterial gene expression data sets provides an unprecedented resource for the study of gene regulation in diverse conditions, but emphasizes the need for self-supervised methods for the automated generation of new hypotheses. One approach for inferring coordinated regulation from bacterial expression data is through neural networks known as denoising autoencoders (DAEs) which encode large datasets in a reduced bottleneck layer. We have generalized this application of DAEs to include deep networks and explore the effects of network architecture on gene set inference using deep learning. We developed a DAE-based pipeline to extract gene sets from transcriptomic data in Escherichia coli, validate our method by comparing inferred gene sets with known pathways, and have used this pipeline to explore how the choice of network architecture impacts gene set recovery. We find that increasing network depth leads the DAEs to explain gene expression in terms of fewer, more concisely defined gene sets, and that adjusting the width results in a tradeoff between generalizability and biological inference. Finally, leveraging our understanding of the impact of DAE architecture, we apply our pipeline to an independent uropathogenic E.coli dataset to identify genes uniquely induced during human colonization. Availability and implementation https://github.com/BarquistLab/DAE_architecture_exploration.
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Affiliation(s)
- Willow Kion-Crosby
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080 Würzburg, Germany
- Department of Biology, University of Toronto, Mississauga, ON L5L 1C6, Canada
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5
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Bittencourt DDC, Brown DM, Assad-Garcia N, Romero MR, Sun L, Palhares de Melo LAM, Freire M, Glass JI. Minimal Bacterial Cell JCVI-syn3B as a Chassis to Investigate Interactions between Bacteria and Mammalian Cells. ACS Synth Biol 2024; 13:1128-1141. [PMID: 38507598 PMCID: PMC11036491 DOI: 10.1021/acssynbio.3c00513] [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: 08/21/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Mycoplasmas are atypical bacteria with small genomes that necessitate colonization of their respective animal or plant hosts as obligate parasites, whether as pathogens, or commensals. Some can grow axenically in specialized complex media yet show only host-cell-dependent growth in cell culture, where they can survive chronically and often through interactions involving surface colonization or internalization. To develop a mycoplasma-based system to identify genes mediating such interactions, we exploited genetically tractable strains of the goat pathogen Mycoplasma mycoides (Mmc) with synthetic designer genomes representing the complete natural organism (minus virulence factors; JCVI-syn1.0) or its reduced counterpart (JCVI-syn3B) containing only those genes supporting axenic growth. By measuring growth of surviving organisms, physical association with cultured human cells (HEK-293T, HeLa), and induction of phagocytosis by human myeloid cells (dHL-60), we determined that JCVI-syn1.0 contained a set of eight genes (MMSYN1-0179 to MMSYN1-0186, dispensable for axenic growth) conferring survival, attachment, and phagocytosis phenotypes. JCVI-syn3B lacked these phenotypes, but insertion of these genes restored cell attachment and phagocytosis, although not survival. These results indicate that JCVI-syn3B may be a powerful living platform to analyze the role of specific gene sets, from any organism, on the interaction with diverse mammalian cells in culture.
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Affiliation(s)
- Daniela
Matias de C. Bittencourt
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
- Embrapa
Genetic Resources and Biotechnology/National Institute of Science
and Technology − Synthetic Biology, Parque Estação
Biológica, PqEB, Av. W5 Norte (final), Brasília, DF 70770-917, Brazil
| | - David M. Brown
- The
J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, Maryland 20850, United States
| | - Nacyra Assad-Garcia
- The
J. Craig Venter Institute, 9605 Medical Center Drive, Suite 150, Rockville, Maryland 20850, United States
| | - Michaela R. Romero
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
| | - Lijie Sun
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
| | - Luis Alberto M. Palhares de Melo
- Embrapa
Genetic Resources and Biotechnology/National Institute of Science
and Technology − Synthetic Biology, Parque Estação
Biológica, PqEB, Av. W5 Norte (final), Brasília, DF 70770-917, Brazil
| | - Marcelo Freire
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
| | - John I. Glass
- The
J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, California 92037, United States
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6
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Banchi E, Corre E, Del Negro P, Celussi M, Malfatti F. Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:126-142. [PMID: 38433960 PMCID: PMC10902248 DOI: 10.1007/s42995-023-00192-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/05/2023] [Indexed: 03/05/2024]
Abstract
Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00192-z.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Erwan Corre
- FR2424, Station Biologique de Roscoff, Plateforme ABiMS (Analysis and Bioinformatics for Marine Science), Sorbonne Université CNRS, 29680 Roscoff, France
| | - Paola Del Negro
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Francesca Malfatti
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
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7
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Özkan M, Yılmaz H, Ergenekon P, Erdoğan EM, Erbakan M. Microbial membrane transport proteins and their biotechnological applications. World J Microbiol Biotechnol 2024; 40:71. [PMID: 38225445 PMCID: PMC10789880 DOI: 10.1007/s11274-024-03891-6] [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: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024]
Abstract
Because of the hydrophobic nature of the membrane lipid bilayer, the majority of the hydrophilic solutes require special transportation mechanisms for passing through the cell membrane. Integral membrane transport proteins (MTPs), which belong to the Major Intrinsic Protein Family, facilitate the transport of these solutes across cell membranes. MTPs including aquaporins and carrier proteins are transmembrane proteins spanning across the cell membrane. The easy handling of microorganisms enabled the discovery of a remarkable number of transport proteins specific to different substances. It has been realized that these transporters have very important roles in the survival of microorganisms, their pathogenesis, and antimicrobial resistance. Astonishing features related to the solute specificity of these proteins have led to the acceleration of the research on the discovery of their properties and the development of innovative products in which these unique properties are used or imitated. Studies on microbial MTPs range from the discovery and characterization of a novel transporter protein to the mining and screening of them in a large transporter library for particular functions, from simulations and modeling of specific transporters to the preparation of biomimetic synthetic materials for different purposes such as biosensors or filtration membranes. This review presents recent discoveries on microbial membrane transport proteins and focuses especially on formate nitrite transport proteins and aquaporins, and advances in their biotechnological applications.
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Affiliation(s)
- Melek Özkan
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye.
| | - Hilal Yılmaz
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Pınar Ergenekon
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Esra Meşe Erdoğan
- Environmental Engineering Department, Gebze Technical University, Kocaeli, 41400, Türkiye
| | - Mustafa Erbakan
- Biosystem Engineering Department, Bozok University, Yozgat , 66900, Türkiye
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8
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Budzinski L, von Goetze V, Chang HD. Single-cell phenotyping of bacteria combined with deep sequencing for improved contextualization of microbiome analyses. Eur J Immunol 2024; 54:e2250337. [PMID: 37863831 DOI: 10.1002/eji.202250337] [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: 04/28/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/22/2023]
Abstract
Great effort was made to characterize the bacterial communities inhabiting the human body as a factor in disease, resulting in the realization that a wide spectrum of diseases is associated with an altered composition of the microbiome. However, the identification of disease-relevant bacteria has been hindered by the high cross-sectional diversity of individual microbiomes, and in most cases, it remains unclear whether the observed alterations are cause or consequence of disease. Hence, innovative analysis approaches are required that enable inquiries of the microbiome beyond mere taxonomic cataloging. This review highlights the utility of microbiota flow cytometry, a single-cell analysis platform to directly interrogate cellular interactions, cell conditions, and crosstalk with the host's immune system within the microbiome to take into consideration the role of microbes as critical interaction partners of the host and the spectrum of microbiome alterations, beyond compositional changes. In conjunction with advanced sequencing approaches it could reveal the genetic potential of target bacteria and advance our understanding of taxonomic diversity and gene usage in the context of the microenvironment. Single-cell bacterial phenotyping has the potential to change our perspective on the human microbiome and empower microbiome research for the development of microbiome-based therapy approaches and personalized medicine.
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Affiliation(s)
- Lisa Budzinski
- Schwiete Laboratory for Microbiota and Inflammation, German Rheumatism Research Centre Berlin - A Leibniz Institute, Berlin, Germany
| | - Victoria von Goetze
- Schwiete Laboratory for Microbiota and Inflammation, German Rheumatism Research Centre Berlin - A Leibniz Institute, Berlin, Germany
| | - Hyun-Dong Chang
- Schwiete Laboratory for Microbiota and Inflammation, German Rheumatism Research Centre Berlin - A Leibniz Institute, Berlin, Germany
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9
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Varela MF, Ortiz-Alegria A, Lekshmi M, Stephen J, Kumar S. Functional Roles of the Conserved Amino Acid Sequence Motif C, the Antiporter Motif, in Membrane Transporters of the Major Facilitator Superfamily. BIOLOGY 2023; 12:1336. [PMID: 37887046 PMCID: PMC10604125 DOI: 10.3390/biology12101336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023]
Abstract
The biological membrane surrounding all living cells forms a hydrophobic barrier to the passage of biologically important molecules. Integral membrane proteins called transporters circumvent the cellular barrier and transport molecules across the cell membrane. These molecular transporters enable the uptake and exit of molecules for cell growth and homeostasis. One important collection of related transporters is the major facilitator superfamily (MFS). This large group of proteins harbors passive and secondary active transporters. The transporters of the MFS consist of uniporters, symporters, and antiporters, which share similarities in structures, predicted mechanism of transport, and highly conserved amino acid sequence motifs. In particular, the antiporter motif, called motif C, is found primarily in antiporters of the MFS. The antiporter motif's molecular elements mediate conformational changes and other molecular physiological roles during substrate transport across the membrane. This review article traces the history of the antiporter motif. It summarizes the physiological evidence reported that supports these biological roles.
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Affiliation(s)
- Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA;
| | - Anely Ortiz-Alegria
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA;
| | - Manjusha Lekshmi
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (M.L.); (J.S.); (S.K.)
| | - Jerusha Stephen
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (M.L.); (J.S.); (S.K.)
| | - Sanath Kumar
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (M.L.); (J.S.); (S.K.)
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10
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Watkin SAJ, Bennie RZ, Gilkes JM, Nock VM, Pearce FG, Dobson RCJ. On the utility of microfluidic systems to study protein interactions: advantages, challenges, and applications. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:459-471. [PMID: 36583735 PMCID: PMC9801160 DOI: 10.1007/s00249-022-01626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022]
Abstract
Within the complex milieu of a cell, which comprises a large number of different biomolecules, interactions are critical for function. In this post-reductionist era of biochemical research, the 'holy grail' for studying biomolecular interactions is to be able to characterize them in native environments. While there are a limited number of in situ experimental techniques currently available, there is a continuing need to develop new methods for the analysis of biomolecular complexes that can cope with the additional complexities introduced by native-like solutions. We think approaches that use microfluidics allow researchers to access native-like environments for studying biological problems. This review begins with a brief overview of the importance of studying biomolecular interactions and currently available methods for doing so. Basic principles of diffusion and microfluidics are introduced and this is followed by a review of previous studies that have used microfluidics to measure molecular diffusion and a discussion of the advantages and challenges of this technique.
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Affiliation(s)
- Serena A J Watkin
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel Z Bennie
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jenna M Gilkes
- Protein Science and Engineering Team, Callaghan Innovation, Christchurch, New Zealand
| | - Volker M Nock
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - F Grant Pearce
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia.
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11
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Stojowska-Swędrzyńska K, Kuczyńska-Wiśnik D, Laskowska E. New Strategies to Kill Metabolically-Dormant Cells Directly Bypassing the Need for Active Cellular Processes. Antibiotics (Basel) 2023; 12:1044. [PMID: 37370363 DOI: 10.3390/antibiotics12061044] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Antibiotic therapy failure is often caused by the presence of persister cells, which are metabolically-dormant bacteria capable of surviving exposure to antimicrobials. Under favorable conditions, persisters can resume growth leading to recurrent infections. Moreover, several studies have indicated that persisters may promote the evolution of antimicrobial resistance and facilitate the selection of specific resistant mutants; therefore, in light of the increasing numbers of multidrug-resistant infections worldwide, developing efficient strategies against dormant cells is of paramount importance. In this review, we present and discuss the efficacy of various agents whose antimicrobial activity is independent of the metabolic status of the bacteria as they target cell envelope structures. Since the biofilm-environment is favorable for the formation of dormant subpopulations, anti-persister strategies should also include agents that destroy the biofilm matrix or inhibit biofilm development. This article reviews examples of selected cell wall hydrolases, polysaccharide depolymerases and antimicrobial peptides. Their combination with standard antibiotics seems to be the most promising approach in combating persistent infections.
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Affiliation(s)
- Karolina Stojowska-Swędrzyńska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dorota Kuczyńska-Wiśnik
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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Blachier F. Amino Acid-Derived Bacterial Metabolites in the Colorectal Luminal Fluid: Effects on Microbial Communication, Metabolism, Physiology, and Growth. Microorganisms 2023; 11:1317. [PMID: 37317289 DOI: 10.3390/microorganisms11051317] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Undigested dietary and endogenous proteins, as well as unabsorbed amino acids, can move from the terminal part of the ileum into the large intestine, where they meet a dense microbial population. Exfoliated cells and mucus released from the large intestine epithelium also supply nitrogenous material to this microbial population. The bacteria in the large intestine luminal fluid release amino acids from the available proteins, and amino acids are then used for bacterial protein synthesis, energy production, and in other various catabolic pathways. The resulting metabolic intermediaries and end products can then accumulate in the colorectal fluid, and their concentrations appear to depend on different parameters, including microbiota composition and metabolic activity, substrate availability, and the capacity of absorptive colonocytes to absorb these metabolites. The aim of the present review is to present how amino acid-derived bacterial metabolites can affect microbial communication between both commensal and pathogenic microorganisms, as well as their metabolism, physiology, and growth.
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Affiliation(s)
- François Blachier
- Université Paris-Saclay, AgroParisTech, INRAe, UMR PNCA, 91120 Palaiseau, France
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Fu WL, Duan PF, Wang Q, Liao YX, Wang YS, Xu MJ, Jiang HH, Zhang X, Rao ZM. Transcriptomics reveals the effect of ammonia nitrogen concentration on Pseudomonas stutzeri F2 assimilation and the analysis of amtB function. Synth Syst Biotechnol 2023; 8:262-272. [PMID: 37033292 PMCID: PMC10074406 DOI: 10.1016/j.synbio.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
The biological treatment of wastewater with high concentrations of ammonia nitrogen has become a hot research issue, but there are limited reports on the mechanism of ammonia nitrogen utilization by microorganisms. In this paper, a transcriptomic approach was used to investigate the differences in gene expression at 500.0 mg/L (Amo 500) and 100.0 mg/L (Amo 100) ammonium concentrations to reveal the mechanism of ammonia nitrogen removal from water by Pseudomonas stutzeri F2. The transcriptome data showed 1015 (459 up-regulated and 556 down-regulated) differentially expressed genes with functional gene annotation related to nitrogen source metabolism, glycolysis, tricarboxylic acid cycle, extracellular polysaccharide synthesis, energy conversion and transmembrane transport, revealing the metabolic process of ammonium nitrogen conversion to biological nitrogen in P. stutzeri F2 through assimilation. To verify the effect of ammonium transporter protein (AmtB) of cell membrane on assimilation, a P. stutzeri F2-ΔamtB mutant strain was obtained by constructing a knockout plasmid (pK18mobsacB-ΔamtB), and it was found that the growth characteristics and ammonium removal rate of the mutant strain were significantly reduced at high ammonium concentration. The carbon source components and dissolved oxygen conditions were optimized after analyzing the transcriptome data, and the ammonium removal rate was increased from 41.23% to 94.92% with 500.0 mg/L ammonium concentration. The study of P. stutzeri F2 transcript level reveals the mechanism of ammonia nitrogen influence on microbial assimilation process and improvement strategy, which provides a new strategy for the treatment of ammonia nitrogen wastewater.
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Ducret V, Gonzalez D, Perron K. Zinc homeostasis in Pseudomonas. Biometals 2022:10.1007/s10534-022-00475-5. [PMID: 36472780 PMCID: PMC10393844 DOI: 10.1007/s10534-022-00475-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
AbstractIn the genus Pseudomonas, zinc homeostasis is mediated by a complete set of import and export systems, whose expression is precisely controlled by three transcriptional regulators: Zur, CzcR and CadR. In this review, we describe in detail our current knowledge of these systems, their regulation, and the biological significance of zinc homeostasis, taking Pseudomonas aeruginosa as our paradigm. Moreover, significant parts of this overview are dedicated to highlight interactions and cross-regulations between zinc and copper import/export systems, and to shed light, through a review of the literature and comparative genomics, on differences in gene complement and function across the whole Pseudomonas genus. The impact and importance of zinc homeostasis in Pseudomonas and beyond will be discussed throughout this review.
Graphical abstract
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15
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Ortega Á, Matilla MA, Krell T. The Repertoire of Solute-Binding Proteins of Model Bacteria Reveals Large Differences in Number, Type, and Ligand Range. Microbiol Spectr 2022; 10:e0205422. [PMID: 36121253 PMCID: PMC9602780 DOI: 10.1128/spectrum.02054-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/24/2022] [Indexed: 12/31/2022] Open
Abstract
Solute-binding proteins (SBPs) are of central physiological relevance for bacteria. They are located in the extracytosolic space, where they present substrates to transporters but also stimulate different types of transmembrane receptors coordinating compound uptake with signal transduction. SBPs are a superfamily composed of proteins recognized by 45 Pfam profiles. The definition of SBP profiles for bacteria is hampered by the fact that these Pfam profiles recognize sensor domains for different types of signaling proteins or cytosolic proteins with alternative functions. We report here the retrieval of the SBPs from 49 bacterial model strains with different lifestyles and phylogenetic distributions. Proteins were manually curated, and the ligands recognized were predicted bioinformatically. There were very large differences in the number and type of SBPs between strains, ranging from 7 SBPs in Helicobacter pylori 26695 to 189 SBPs in Sinorhizobium meliloti 1021. SBPs were found to represent 0.22 to 5.13% of the total protein-encoding genes. The abundance of SBPs was largely determined by strain phylogeny, and no obvious link with the bacterial lifestyle was noted. Most abundant (36%) were SBPs predicted to recognize amino acids or peptides, followed by those expected to bind different sugars (18%). To the best of our knowledge, this is the first comparative study of bacterial SBP repertoires. Given the importance of SBPs in nutrient uptake and signaling, this study enhances the knowledge of model bacteria and will permit the definition of SBP profiles of other strains. IMPORTANCE SBPs are essential components for many transporters, but multiple pieces of more recent evidence indicate that the SBP-mediated stimulation of different transmembrane receptors is a general and widespread signal transduction mechanism in bacteria. The double function of SBPs in coordinating transport with signal transduction remains to a large degree unexplored and represents a major research need. The definition of the SBP repertoire of the 49 bacterial model strains examined here, along with information on their cognate ligand profiles forms the basis to close this gap in knowledge. Furthermore, this study provides information on the forces that have driven the evolution of transporters with different ligand specificities in bacteria that differ in phylogenetics and lifestyle. This article is also a first step in setting up automatic algorithms that permit the large-scale identification of the SBP repertoire in proteomes.
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Affiliation(s)
- Álvaro Ortega
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence Campus Mare Nostrum, Murcia, Spain
| | - Miguel A. Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Luo W, Wang J, Chen Y, Wang Y, Li R, Tang J, Geng F. Quantitative proteomic analysis provides insight into the survival mechanism of Salmonella typhimurium under high-intensity ultrasound treatment. Curr Res Food Sci 2022; 5:1740-1749. [PMID: 36268134 PMCID: PMC9576580 DOI: 10.1016/j.crfs.2022.09.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/21/2022] [Accepted: 09/30/2022] [Indexed: 11/21/2022] Open
Abstract
The survival mechanism of Salmonella treated with high-intensity ultrasound (HIU) should be explored to further enhance the bactericidal efficacy of HIU. In this study, culturable Salmonella was reduced by applying HIU. Electron microscope imaging revealed that HIU caused the disintegration of cell structure and leakage of intracellular substances. For the Salmonella after the HIU treatment, key enzymes of the tricarboxylic acid [TCA] cycle were significantly downregulated, which led to a reduced ATP content (45.25%–75.00%), although ATPase activity was augmented by 33.82%–60.64% in the Salmonella. Accordingly, surviving Salmonella could have tolerated the stress of HIU by upregulating their environmental sensing (two-component system), chemotaxis (bacterial chemotaxis), substance uptake (ABC transporter), and ATP production (oxidative phosphorylation). Therefore, synergistically blocking the ATP production, signal transduction, or substance intake of Salmonella offer promising potential strategies to improve the bactericidal effect of HIU in industrial food processing. Cell damage and substances leakage were observed in ultrasound treated Salmonella. Ultrasonic treatments caused 1017 differentially expressed proteins in Salmonella. Ultrasound inhibited tricarboxylic acid cycle and reduced adenosine triphosphate content in Salmonella. Salmonella tolerated ultrasound by upregulating two-component system, ABC transport, and bacterial chemotaxis. These altered pathways could be potential targets to enhance the lethality of ultrasound.
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Affiliation(s)
- Wei Luo
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Jinqiu Wang
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Yan Chen
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Yixu Wang
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Rui Li
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plants, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Jie Tang
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China
| | - Fang Geng
- Institute for Egg Science and Technology, School of Food and Biological Engineering, Chengdu University, No. 2025 Chengluo Avenue, Chengdu, 610106, China,Corresponding author.
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Lu Y, Liu JH, Yue C, Bergen PJ, Wu R, Li J, Liu YY. Overexpression of mcr-1 disrupts cell envelope synthesis and causes the dysregulation of carbon metabolism, redox balance and nucleic acids. Int J Antimicrob Agents 2022; 60:106643. [PMID: 35872294 DOI: 10.1016/j.ijantimicag.2022.106643] [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: 01/07/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/05/2022]
Abstract
Rapid dissemination of plasmid-borne polymyxin resistance mcr-1 genes threatens the efficacy of polymyxins. Acquisition of mcr-1 imposes a fitness cost on bacteria. The identification of the molecular mechanisms underpinning this fitness cost will help in the development of adjunctive antimicrobial therapies that target polymyxin-resistant Gram-negative pathogens. We employed phenotypic assays and transcriptomics to investigate the impact of mcr-1 expression on membrane characteristics and transcriptomic responses in E. coli TOP10 carrying the empty vector pBAD (TOP10+pBAD) and harboring pBAD-mcr-1 (TOP10+pBAD-mcr-1). The overexpression of mcr-1 increased outer membrane permeability and caused membrane depolarization, reflective of the transcriptomic results that showed downregulation of multiple genes involved in lipopolysaccharide core and O-antigen biosynthesis. Overexpression of mcr-1 also caused considerable gene expression changes in pathways involving carbohydrate metabolism (phosphotransferase system, pentose phosphate pathway, and pantothenate and coenzyme A biosynthesis), ABC transporters and intracellular responses to stress, especially those associated with oxidative and nucleic acid damage. Expression of mcr-1 also triggered the production of reactive oxygen species. Collectively, these findings indicate that overexpression of mcr-1 results in persistent transcriptomic changes that primarily involve disruption to cell envelope synthesis via the reduction of LPS modifications, as well as dysregulation of carbon metabolism, redox balance and nucleic acids. These consequences of expression dysregulation may act as the main factors that impose a fitness cost with mcr-1 expression.
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Affiliation(s)
- Yaoyao Lu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jian-Hua Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Chao Yue
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Phillip J Bergen
- Biomedicine Discovery Institute and Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Renjie Wu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Jian Li
- Biomedicine Discovery Institute and Department of Microbiology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia.
| | - Yi-Yun Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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Bioremediation potential of hexavalent chromium-resistant Arthrobacter globiformis 151B: study of the uptake of cesium and other alkali ions. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2022; 25:745-758. [PMID: 35768673 DOI: 10.1007/s10123-022-00258-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/04/2022] [Accepted: 06/07/2022] [Indexed: 10/17/2022]
Abstract
Cesium (Cs+) enters environments largely because of global release into the environment from weapons testing and accidents such as Fukushima Daiichi and Chernobyl nuclear waste. Even at low concentrations, Cs+ is highly toxic to ecological receptors because of its physicochemical similarity to macronutrient potassium (K+). We investigated the uptake and accumulation of Cs+ by Arthrobacter globiformis strain 151B in reference to three similar alkali metal cations rubidium (Rb+), sodium (Na+), and potassium (K+). The impact of hexavalent chromium (Cr+6) as a co-contaminant was also evaluated. A. globiformis 151B accumulated Cs+ and Cr6+ in a time-dependent fashion. In contrast, the uptake and accumulation of Rb+ did not exhibit any trends. An exposure to Cs+, Rb+, and Cr+6 triggered a drastic increase in K+ and Na+ uptake by the bacterial cells. That was followed by the efflux of K+ and Na+, suggesting a Cs+ "substitution." Two-dimensional gel-electrophoresis of bacterial cell proteomes with the following mass-spectrometry of differentially expressed bands revealed that incubation of bacterial cells with Cs+ induced changes in the expression of proteins involved in the maintenance of cellular homeostasis and reactive oxygen species removal. The ability of A. globiformis 151B to mediate the uptake and accumulation of cesium and hexavalent chromium suggests that it possesses wide-range bioremediation potential.
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Liu H, Liu ZH, Zhang RK, Yuan JS, Li BZ, Yuan YJ. Bacterial conversion routes for lignin valorization. Biotechnol Adv 2022; 60:108000. [DOI: 10.1016/j.biotechadv.2022.108000] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 12/12/2022]
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Adaptation Potential of Three Psychrotolerant Aquatic Bacteria in the Pan-Okhotsk Region. WATER 2022. [DOI: 10.3390/w14071107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Pan-Okhotsk region, which is part of the western North Pacific Ocean, is famous for its active volcanoes, which are part of the Pacific Ring of Fire and that enrich the surrounding waters with essential chemicals. Therefore, this region, including the Sea of Okhotsk and the Sea of Japan, is characterized by rich biota. Bacterioplankton plays a significant part in biological communities and is an indicator of ecosystem function. Analyzing the adaptability of three representatives of the microbiota of the Pan-Okhotsk region was the goal of our investigation. Marinomonas primoryensis KMM3633T (MP), Yersinia ruckeri KMM821 (YR), and Yersinia pseudotuberculosis 598 (YP) from the G.B. Elyakov Pacific Institute of Bioorganic Chemistry were studied by means of genomic and bioinformatic methods. The list of membrane translocator proteins, metabolism pathways, and cold shock and antifreeze proteins that were revealed in the genome of MP characterized this bacterium as being adaptable to free living in marine conditions, even at winter temperatures. The genomic potential of YR and YP makes not only survival in the environment of the Pan-Okhotsk region but also pathogenesis in eukaryotic organisms possible. The data obtained will serve as a basis for further ecosystem monitoring with the help of microbiota research.
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21
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Arif T, Currie MJ, Dobson RCJ, Newson HL, Poonthiyil V, Fairbanks AJ, North RA, Rendle PM. Synthesis of N-acetylmannosamine-6-phosphate derivatives to investigate the mechanism of N-acetylmannosamine-6-phosphate 2-epimerase. Carbohydr Res 2021; 510:108445. [PMID: 34607125 DOI: 10.1016/j.carres.2021.108445] [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: 07/06/2021] [Revised: 09/14/2021] [Accepted: 09/21/2021] [Indexed: 11/19/2022]
Abstract
The synthesis of analogues of natural enzyme substrates can be used to help deduce enzymatic mechanisms. N-Acetylmannosamine-6-phosphate 2-epimerase is an enzyme in the bacterial sialic acid catabolic pathway. To investigate whether the mechanism of this enzyme involves a re-protonation mechanism by the same neighbouring lysine that performed the deprotonation or a unique substrate-assisted proton displacement mechanism involving the substrate C5 hydroxyl, the syntheses of two analogues of the natural substrate, N-acetylmannosamine-6-phosphate, are described. In these novel analogues, the C5 hydroxyl has been replaced with a proton and a methyl ether respectively. As recently reported, Staphylococcus aureus N-acetylmannosamine-6-phosphate 2-epimerase was co-crystallized with these two compounds. The 5-deoxy variant bound to the enzyme active site in a different orientation to the natural substrate, while the 5-methoxy variant did not bind, adding to the evidence that this enzyme uses a substrate-assisted proton displacement mechanism. This mechanistic information may help in the design of potential antibacterial drug candidates.
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Affiliation(s)
- Tanzeel Arif
- Ferrier Research Institute, Victoria University of Wellington, PO Box 33-436, Lower Hutt, 5046, New Zealand
| | - Michael J Currie
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Renwick C J Dobson
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Harriet L Newson
- Ferrier Research Institute, Victoria University of Wellington, PO Box 33-436, Lower Hutt, 5046, New Zealand
| | - Vivek Poonthiyil
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Antony J Fairbanks
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Rachel A North
- University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Phillip M Rendle
- Ferrier Research Institute, Victoria University of Wellington, PO Box 33-436, Lower Hutt, 5046, New Zealand.
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