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Ulmann N, Hioe J, Touraud D, Horinek D, Kunz W. Self-association as a solubility limiting factor of riboflavin in aqueous media. Phys Chem Chem Phys 2024; 26:18930-18942. [PMID: 38952212 DOI: 10.1039/d4cp02074j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Single crystal X-ray diffraction analysis of needle shaped riboflavin (RF) crystals revealed π-stacking of RF's isoalloxazine units (distance: 3.643-3.313 Å) with syn-orientated ribityl chains. In line with this, classical molecular dynamics (MD) (400 ns) using an isobaric-isothermal (NPT) ensemble of eight RF in a water box (〈V〉 ∼ 508.62 nm3, 〈p〉 = 1.11 bar) revealed anti-aligned aggregation of RF in water (COM-distance: 4 Å). Comparing umbrella sampling for the separation of two RF molecules to the separation of two lumichrome molecules, the similar mean potential force for the separation of RF and lumichrome (22.8 kJ mol-1; 24.4 kJ mol-1) proved dispersive interactions as the origin of RF's aggregation. Though stacking of RF is the major water-solubility limiting factor, the conformation of RF's ribityl chain may alter the solubility in water. Both, MD (in water) and COSMO-RS (in water continuum) predicted that conformations of RF with an extended ribityl chain are thermodynamically preferred over any conformations with internal hydrogen bonds between hydroxyl groups and nitrogen/oxygen atoms of the pyrimidine moiety of the flavin ring. Interestingly, COSMO-RS predicted the solubility of the extended conformation to be significantly lower than the latter leading to the very low average solubility of RF. Nuclear Overhauser effect measurements (NOESY) of the structurally related sodium riboflavin 5'-monophosphate (RF-PO4) in deuterium oxide confirmed π-stacking of the isoalloxazine rings. In conformity with the 350 times higher water-solubility of RF-PO4, NOESY also indicated a contorted conformation of the ribityl phosphate chain, whereas, for RF, indications for a contorted chain were not observed.
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Affiliation(s)
- Nadja Ulmann
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
| | - Johnny Hioe
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
| | - Didier Touraud
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
| | - Dominik Horinek
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
| | - Werner Kunz
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.
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2
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Reis PCJ, Tsuji JM, Weiblen C, Schiff SL, Scott M, Stein LY, Neufeld JD. Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats. THE ISME JOURNAL 2024; 18:wrae041. [PMID: 38470309 PMCID: PMC11008690 DOI: 10.1093/ismejo/wrae041] [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: 10/09/2023] [Revised: 01/06/2024] [Accepted: 03/13/2024] [Indexed: 03/13/2024]
Abstract
Methanotrophic bacteria mitigate emissions of the potent greenhouse gas methane (CH4) from a variety of anthropogenic and natural sources, including freshwater lakes, which are large sources of CH4 on a global scale. Despite a dependence on dioxygen (O2) for CH4 oxidation, abundant populations of putatively aerobic methanotrophs have been detected within microoxic and anoxic waters and sediments of lakes. Experimental work has demonstrated active aerobic methanotrophs under those conditions, but how they are able to persist and oxidize CH4 under O2 deficiency remains enigmatic. In this review, we discuss possible mechanisms that underpin the persistence and activity of aerobic methanotrophs under O2-limiting conditions in freshwater habitats, particularly lakes, summarize experimental evidence for microbial oxidation of CH4 by aerobic bacteria under low or no O2, and suggest future research directions to further explore the ecology and metabolism of aerobic methanotrophs in O2-limiting environments.
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Affiliation(s)
- Paula C J Reis
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Jackson M Tsuji
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Cerrise Weiblen
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sherry L Schiff
- Department of Earth & Environmental Sciences, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Matthew Scott
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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3
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Wang Y, Ling N, Wang Y, Ou D, Liang Z, Li G, Zhao H, Ye Y. Effect of ferric ions on Cronobacter sakazakii growth, biofilm formation, and swarming motility. Int J Food Microbiol 2024; 408:110418. [PMID: 37857020 DOI: 10.1016/j.ijfoodmicro.2023.110418] [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: 05/17/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/21/2023]
Abstract
Cronobacter sakazakii (C. sakazakii) is a common food-borne pathogen that induces meningitis, sepsis, and necrotizing enterocolitis, primarily in newborns and infants. Iron plays a pivotal role in the growth of cells and biofilm formation. However, the effects of hemin (ferric ion donor) on C. sakazakii cells are scarcely known. Here, we explored the effect of ferric ions on the growth of planktonic C. sakazakii, biofilm formation, and swarming motility by crystal violet staining (CVS), scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), and swarming assay. Our study demonstrated that ferric ions facilitated the growth of planktonic C. sakazakii, while hemin at concentrations ranging from 50 to 800 μmol/L promoted biofilm formation and at concentrations between 50 and 200 μmol/L enhanced the swarming motility of C. sakazakii. Furthermore, high hemin concentrations (400-800 μmol/L) were found to reduce flagellar length, as confirmed by transmission electron microscopy (TEM). These findings indicated that ferric ions mediated the swarming motility of C. sakazakii by regulating flagellar assembly. Finally, transcriptomic analysis of C. sakazakii was performed at hemin concentrations of 0, 50, and 200 μmol/L, which revealed that several genes associated with iron transport and metabolism, and flagellar assembly were essential for the survival of C. sakazakii under hemin treatment. Our findings revealed the molecular basis of ferric ions on C. sakazakii growth and biofilm formation, thus providing a novel perspective for its prevention and control.
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Affiliation(s)
- Yang Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Na Ling
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Yaping Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Dexin Ou
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Zhao Liang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Guoqing Li
- Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Hongyuan Zhao
- Institute of Horticulture Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
| | - Yingwang Ye
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China.
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4
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Deng Y, Liang C, Zhu X, Zhu X, Chen L, Pan H, Xun F, Tao Y, Xing P. Methylomonadaceae was the active and dominant methanotroph in Tibet lake sediments. ISME COMMUNICATIONS 2024; 4:ycae032. [PMID: 38524764 PMCID: PMC10960969 DOI: 10.1093/ismeco/ycae032] [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: 01/03/2024] [Revised: 02/21/2024] [Accepted: 02/29/2024] [Indexed: 03/26/2024]
Abstract
Methane (CH4), an important greenhouse gas, significantly impacts the local and global climate. Our study focused on the composition and activity of methanotrophs residing in the lakes on the Tibetan Plateau, a hotspot for climate change research. Based on the field survey, the family Methylomonadaceae had a much higher relative abundance in freshwater lakes than in brackish and saline lakes, accounting for ~92% of total aerobic methanotrophs. Using the microcosm sediment incubation with 13CH4 followed by high throughput sequencing and metagenomic analysis, we further demonstrated that the family Methylomonadaceae was actively oxidizing CH4. Moreover, various methylotrophs, such as the genera Methylotenera and Methylophilus, were detected in the 13C-labeled DNAs, which suggested their participation in CH4-carbon sequential assimilation. The presence of CH4 metabolism, such as the tetrahydromethanopterin and the ribulose monophosphate pathways, was identified in the metagenome-assembled genomes of the family Methylomonadaceae. Furthermore, they had the potential to adapt to oxygen-deficient conditions and utilize multiple electron acceptors, such as metal oxides (Fe3+), nitrate, and nitrite, for survival in the Tibet lakes. Our findings highlighted the predominance of Methylomonadaceae and the associated microbes as active CH4 consumers, potentially regulating the CH4 emissions in the Tibet freshwater lakes. These insights contributed to understanding the plateau carbon cycle and emphasized the significance of methanotrophs in mitigating climate change.
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Affiliation(s)
- Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Chulin Liang
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xiaomeng Zhu
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xinshu Zhu
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Lei Chen
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Hongan Pan
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Fan Xun
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ye Tao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China
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5
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Garcez DCP, Ribeiro G, Kominkiewicz M, da Costa MM, Chideroli RT, Rosa DS, Dos Santos IEP, Morante VHP, Silveira S, Girardini LK. Synergy between polypyrrol and benzoic acid against antibiotic-resistant Salmonella spp. J Appl Microbiol 2023; 134:lxad186. [PMID: 37656886 DOI: 10.1093/jambio/lxad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/30/2023] [Accepted: 08/25/2023] [Indexed: 09/03/2023]
Abstract
AIMS The purpose was to characterize Salmonella Heidelberg (SH) and Minnesota (SM) isolates in terms of their resistance and persistence profile and to assess the antimicrobial effect of benzoic acid (BA) and polypyrrole (PPy). METHODS AND RESULTS The 20 isolates from broiler litter drag swabs were submitted to antibiogram and efflux pump expression. The minimum inhibitory/bactericidal concentration (MIC/MBC) of the compounds, synergistic activity, time kill, biofilm production, presence of related genes, and molecular docking between compounds and bacterial target sites were evaluated. All isolates showed multidrug resistance (MDR) and BA and PPy showed mean MIC (1750 and 342 µg ml-1) and MBC (3167 and 1000 µg ml-1), respectively. None of the isolates expressed an efflux pump. The compounds showed synergism against an SH isolate and reduced the count by 3 logs in the presence of the compounds after 4 h. Most isolates (16/20) produced weak to moderate biofilm and 17 showed genes related to biofilm. The compounds interacted with two essential proteins, 3,4-dihydroxy-2-butanone 4-phosphate synthase proteins and ferritin-like domain-containing protein, in bacterial metabolism at different target sites. CONCLUSIONS It can be concluded that BA and PPy showed activity on SH and SM, MDR, and biofilm producers, with a potential synergistic effect.
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Affiliation(s)
| | - Gabrielle Ribeiro
- University of West Santa Catarina (UNOESC), Xanxerê, State of Santa Catarina, 89600-000, Brazil
| | - Marcelo Kominkiewicz
- University of West Santa Catarina (UNOESC), Xanxerê, State of Santa Catarina, 89600-000, Brazil
| | - Mateus Matiuzzi da Costa
- Federal University of the São Francisco Valley (UNIVASF), Petrolina, State of Pernambuco, 56304-205, Brazil
| | - Roberta Torres Chideroli
- Federal University of the São Francisco Valley (UNIVASF), Petrolina, State of Pernambuco, 56304-205, Brazil
| | - Danillo Sales Rosa
- Federal Rural University of Pernambuco (UFRPE), Recife, State of Pernambuco, 52171-030, Brazil
| | | | | | - Simone Silveira
- University of West Santa Catarina (UNOESC), Xanxerê, State of Santa Catarina, 89600-000, Brazil
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6
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Brooks SM, Marsan C, Reed KB, Yuan SF, Nguyen DD, Trivedi A, Altin-Yavuzarslan G, Ballinger N, Nelson A, Alper HS. A tripartite microbial co-culture system for de novo biosynthesis of diverse plant phenylpropanoids. Nat Commun 2023; 14:4448. [PMID: 37488111 PMCID: PMC10366228 DOI: 10.1038/s41467-023-40242-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023] Open
Abstract
Plant-derived phenylpropanoids, in particular phenylpropenes, have diverse industrial applications ranging from flavors and fragrances to polymers and pharmaceuticals. Heterologous biosynthesis of these products has the potential to address low, seasonally dependent yields hindering ease of widespread manufacturing. However, previous efforts have been hindered by the inherent pathway promiscuity and the microbial toxicity of key pathway intermediates. Here, in this study, we establish the propensity of a tripartite microbial co-culture to overcome these limitations and demonstrate to our knowledge the first reported de novo phenylpropene production from simple sugar starting materials. After initially designing the system to accumulate eugenol, the platform modularity and downstream enzyme promiscuity was leveraged to quickly create avenues for hydroxychavicol and chavicol production. The consortia was found to be compatible with Engineered Living Material production platforms that allow for reusable, cold-chain-independent distributed manufacturing. This work lays the foundation for further deployment of modular microbial approaches to produce plant secondary metabolites.
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Affiliation(s)
- Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Celeste Marsan
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Kevin B Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Shuo-Fu Yuan
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Dustin-Dat Nguyen
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Adit Trivedi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Gokce Altin-Yavuzarslan
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, 98195, USA
| | - Nathan Ballinger
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, USA
| | - Alshakim Nelson
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, 98195, USA
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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7
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Li B, Tao Y, Mao Z, Gu Q, Han Y, Hu B, Wang H, Lai A, Xing P, Wu QL. Iron oxides act as an alternative electron acceptor for aerobic methanotrophs in anoxic lake sediments. WATER RESEARCH 2023; 234:119833. [PMID: 36889095 DOI: 10.1016/j.watres.2023.119833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Conventional aerobic CH4-oxidizing bacteria (MOB) are frequently detected in anoxic environments, but their survival strategy and ecological contribution are still enigmatic. Here we explore the role of MOB in enrichment cultures under O2 gradients and an iron-rich lake sediment in situ by combining microbiological and geochemical techniques. We found that enriched MOB consortium used ferric oxides as alternative electron acceptors for oxidizing CH4 with the help of riboflavin when O2 was unavailable. Within the MOB consortium, MOB transformed CH4 to low molecular weight organic matter such as acetate for consortium bacteria as a carbon source, while the latter secrete riboflavin to facilitate extracellular electron transfer (EET). Iron reduction coupled to CH4 oxidation mediated by the MOB consortium was also demonstrated in situ, reducing 40.3% of the CH4 emission in the studied lake sediment. Our study indicates how MOBs survive under anoxia and expands the knowledge of this previously overlooked CH4 sink in iron-rich sediments.
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Affiliation(s)
- Biao Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ye Tao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhendu Mao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Qiujin Gu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yixuan Han
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Hongwei Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Anxing Lai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
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8
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Verma M, Singh V, Mishra V. Moving towards the enhancement of extracellular electron transfer in electrogens. World J Microbiol Biotechnol 2023; 39:130. [PMID: 36959310 DOI: 10.1007/s11274-023-03582-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
Electrogens are very common in nature and becoming a contemporary theme for research as they can be exploited for extracellular electron transfer. Extracellular electron transfer is the key mechanism behind bioelectricity generation and bioremediation of pollutants via microbes. Extracellular electron transfer mechanisms for electrogens other than Shewanella and Geobacter are less explored. An efficient extracellular electron transfer system is crucial for the sustainable future of bioelectrochemical systems. At present, the poor extracellular electron transfer efficiency remains a decisive factor in limiting the development of efficient bioelectrochemical systems. In this review article, the EET mechanisms in different electrogens (bacteria and yeast) have been focused. Apart from the well-known electron transfer mechanisms of Shewanella oneidensis and Geobacter metallireducens, a brief introduction of the EET pathway in Rhodopseudomonas palustris TIE-1, Sideroxydans lithotrophicus ES-1, Thermincola potens JR, Lysinibacillus varians GY32, Carboxydothermus ferrireducens, Enterococcus faecalis and Saccharomyces cerevisiae have been included. In addition to this, the article discusses the several approaches to anode modification and genetic engineering that may be used in order to increase the rate of extracellular electron transfer. In the side lines, this review includes the engagement of the electrogens for different applications followed by the future perspective of efficient extracellular electron transfer.
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Affiliation(s)
- Manisha Verma
- School of Biochemical Engineering, IIT (BHU), 221005, Varanasi, India
| | - Vishal Singh
- School of Biochemical Engineering, IIT (BHU), 221005, Varanasi, India
| | - Vishal Mishra
- School of Biochemical Engineering, IIT (BHU), 221005, Varanasi, India.
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9
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Wang Y, Ge H, Xiao Z, Huang C, Wang G, Duan X, Zheng L, Dong J, Huang X, Zhang Y, An H, Xu W, Wang Y. Spatial Proteome Reorganization of a Photosynthetic Model Cyanobacterium in Response to Abiotic Stresses. J Proteome Res 2023; 22:1255-1269. [PMID: 36930737 DOI: 10.1021/acs.jproteome.2c00759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Spatial proteome reorganization in response to a changing environment represents a different layer of adaptation mechanism in addition to differential expression of a subset of stress responsive genes in photosynthetic organisms. Profiling such reorganization events is critically important to extend our understanding how photosynthetic organisms adapt to adverse environments. Thus, we treated a unicellular photosynthetic model cyanobacterium, Synechocystis sp. PCC 6803 (hereafter referred to as Synechocystis), with five different types of abiotic stresses including nitrogen starvation, iron deficiency, cold, heat, and darkness, and systematically identified proteins showing stress-induced differential expression and/or redistribution between the membrane and the soluble fractions using a quantitative proteomics approach. A number of proteins showing such a redistribution in response to a single or multiple types of abiotic stresses were identified. These include 12 ribosomal proteins displaying unanimous cold-induced redistribution to the membrane and the protein FurA, a master regulator of iron acquisition, displaying iron deficiency- and nitrogen starvation-induced redistribution to the membrane. Such findings shed light on a novel regulatory mechanism underlying the corresponding stress responses, and establish the results in the present study as an important resource for future studies intended to understand how photosynthetic organisms cope with adverse environments.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Zhen Xiao
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Gaojie Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Xiaoxiao Duan
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Limin Zheng
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Jinghui Dong
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Hongyu An
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
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10
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Lai YH, Franke R, Pinkert L, Overwin H, Brönstrup M. Molecular Signatures of the Eagle Effect Induced by the Artificial Siderophore Conjugate LP-600 in E. coli. ACS Infect Dis 2023; 9:567-581. [PMID: 36763039 PMCID: PMC10012262 DOI: 10.1021/acsinfecdis.2c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Achieving cellular uptake is a central challenge for novel antibiotics targeting Gram-negative bacterial pathogens. One strategy is to hijack the bacterial iron transport system by siderophore-antibiotic conjugates that are actively imported into the cell. This was realized with the MECAM-ampicillin conjugate LP-600 we recently reported that was highly active against E. coli. In the present study, we investigate a paradoxical regrowth of E. coli upon treatment of LP-600 at concentrations 16-32 times above the minimum inhibitory concentration (MIC). The phenomenon, coined "Eagle-effect" in other systems, was not due to resistance formation, and it occurred for the siderophore conjugate but not for free ampicillin. To investigate the molecular imprint of the Eagle effect, a combined transcriptome and untargeted metabolome analysis was conducted. LP-600 induced the expression of genes involved in iron acquisition, SOS response, and the e14 prophage upon regrowth conditions. The Eagle effect was diminished in the presence of sulbactam, which we ascribe to a putative synergistic antibiotic action but not to β-lactamase inhibition. The study highlights the relevance of the Eagle effect for siderophore conjugates. Through the first systematic -omics investigations, it also demonstrates that the Eagle effect manifests not only in a paradoxical growth but also in unique gene expression and metabolite profiles.
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Affiliation(s)
- Yi-Hui Lai
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Lukas Pinkert
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Heike Overwin
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, 38124 Braunschweig, Germany.,Center of Biomolecular Drug Research (BMWZ), Leibniz University, 30159 Hannover, Germany
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11
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Bustin KA, Abbas A, Wang X, Abt MC, Zackular JP, Matthews ML. Characterizing metabolic drivers of Clostridioides difficile infection with activity-based hydrazine probes. Front Pharmacol 2023; 14:1074619. [PMID: 36778002 PMCID: PMC9908766 DOI: 10.3389/fphar.2023.1074619] [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: 10/19/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023] Open
Abstract
Many enzymes require post-translational modifications or cofactor machinery for primary function. As these catalytically essential moieties are highly regulated, they act as dual sensors and chemical handles for context-dependent metabolic activity. Clostridioides difficile is a major nosocomial pathogen that infects the colon. Energy generating metabolism, particularly through amino acid Stickland fermentation, is central to colonization and persistence of this pathogen during infection. Here using activity-based protein profiling (ABPP), we revealed Stickland enzyme activity is a biomarker for C. difficile infection (CDI) and annotated two such cofactor-dependent Stickland reductases. We structurally characterized the cysteine-derived pyruvoyl cofactors of D-proline and glycine reductase in C. difficile cultures and showed through cofactor monitoring that their activity is regulated by their respective amino acid substrates. Proline reductase was consistently active in toxigenic C. difficile, confirming the enzyme to be a major metabolic driver of CDI. Further, activity-based hydrazine probes were shown to be active site-directed inhibitors of proline reductase. As such, this enzyme activity, via its druggable cofactor modality, is a promising therapeutic target that could allow for the repopulation of bacteria that compete with C. difficile for proline and therefore restore colonization resistance against C. difficile in the gut.
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Affiliation(s)
- Katelyn A. Bustin
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Arwa Abbas
- Division of Protective Immunity, Children’s Hospital of Pennsylvania, Philadelphia, PA, United States
| | - Xie Wang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Michael C. Abt
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Joseph P. Zackular
- Division of Protective Immunity, Children’s Hospital of Pennsylvania, Philadelphia, PA, United States,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Megan L. Matthews
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States,*Correspondence: Megan L. Matthews,
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12
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Wang C, Zhang J, Guo G, Huo W, Xia CQ, Chen L, Zhang Y, Pei C, Liu Q. Effects of folic acid and riboflavin on growth performance, nutrient digestion and rumen fermentation in Angus bulls. Br J Nutr 2023; 129:1-9. [PMID: 35225178 DOI: 10.1017/s0007114522000630] [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] [Indexed: 11/07/2022]
Abstract
This study examined the influences of coated folic acid (CFA) and coated riboflavin (CRF) on bull performance, nutrients digestion and ruminal fermentation. Forty-eight Angus bulls based on a randomised block and 2 × 2 factorial design were assigned to four treatments. The CFA of 0 or 6 mg of folic acid/kg DM was supplemented in diets with CRF 0 or 60 mg riboflavin (RF)/kg DM. Supplementation of CRF in diets with CFA had greater increase in daily weight gain and feed efficiency than in diets without CFA. Supplementation with CFA or CRF enhanced digestibility of DM, organic matter, crude protein, neutral-detergent fibre and non-fibre carbohydrate. Ruminal pH and ammonia N content decreased and total volatile fatty acids concentration and acetate to propionate ratio elevated for CFA or CRF addition. Supplement of CFA or CRF increased the activities of fibrolytic enzymes and the numbers of total bacteria, protozoa, fungi, dominant fibrolytic bacteria and Prevotella ruminicola. The activities of α-amylase, protease and pectinase and the numbers of Butyrivibrio fibrisolvens and Ruminobacter amylophilus were increased by CFA but were unaffected by CRF. Blood concentration of folate elevated and homocysteine decreased for CFA addition. The CRF supplementation elevated blood concentrations of folate and RF. These findings suggested that CFA or CRF inclusion had facilitating effects on performance and ruminal fermentation, and combined addition of CFA and CRF had greater increase in performance than CFA or CRF addition alone in bulls.
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Affiliation(s)
- Cong Wang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, P. R. People's Republic of China
| | - Jing Zhang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, P. R. People's Republic of China
| | - Gang Guo
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, P. R. People's Republic of China
| | - Wenjie Huo
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, P. R. People's Republic of China
| | - Cheng Qiang Xia
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, P. R. People's Republic of China
| | - Lei Chen
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, P. R. People's Republic of China
| | - Yawei Zhang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, P. R. People's Republic of China
| | - Caixia Pei
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, P. R. People's Republic of China
| | - Qiang Liu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, P. R. People's Republic of China
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13
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Liu J, Lin H, Cao M, Lin T, Lin A, Xu W, Wang H, He J, Li Y, Tang H, Zhang B. Shifts and importance of viable bacteria in treatment of DSS-induced ulcerative colitis mice with FMT. Front Cell Infect Microbiol 2023; 13:1124256. [PMID: 36814445 PMCID: PMC9939747 DOI: 10.3389/fcimb.2023.1124256] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Background and Aims Ulcerative colitis (UC) has become a global public health concern, and is in urgent need of novel therapies. Fecal microbiota transplantation (FMT) targeting gut microbiota has recently been applied to the treatment of UC. Despite its recent successes, it is still largely unknown how FMT functionally modulates the gut microbiota and improves the disease. Methods We prospectively collected fecal samples from the 40 mice (30 mice for dextran sulfate sodium (DSS)-induced, 10 for controls), followed by Propidium monoazide treatment for 16S rRNA gene sequencing. These 30 mice were divided equally into 3 groups, which were transplanted with original donor microbiota (DO), inactivated donor microbiota (DI) and saline, respectively. Subsequently, we used 16S rRNA gene sequencing to analyze the viable gut bacteria of ulcerative colitis (UC) mice and histological analysis to evaluate the effects of fecal microbiota transplantation (FMT) with viable microbiota. Results We demonstrated that the community structure of viable bacteria was significantly different from fecal bacteria based on total DNA. Furthermore, the intestinal viable microbiota and colonic mucosal structure of mice were significantly changed by DSS induction. The histological analysis showed that only the mice treated with original donor microbiota group (HF) achieved a significant improvement. Compared with inactivated donor microbiota group (IF) and saline (NF), Lactobacillus and Halomonas were significantly enriched in the HF group. Conclusion We inferred that only live bacteria from human donor reversed the histopathology and symptoms of UC in mice and altered the gut microbiota. The activity of gut microbiota in donor samples should be considered in FMT and that detailed analysis of viable microbiota is essential to understand the mechanisms by which FMT produces therapeutic effects in the future.
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Affiliation(s)
- Jinglong Liu
- Department of Gastroenterology, Shanxi Provincial People’s Hospital, Taiyuan, China
| | - Hao Lin
- Center for Microecological Medical Technology, Xiamen Institute of Union Respiratory Health, Xiamen, China
| | - Man Cao
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Tan Lin
- Center for Microecological Medical Technology, Xiamen Institute of Union Respiratory Health, Xiamen, China
| | - Aiqiang Lin
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Wei Xu
- Center for Microecological Medical Technology, Xiamen Institute of Union Respiratory Health, Xiamen, China
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Han Wang
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Jianquan He
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Yuantao Li
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
- *Correspondence: Yuantao Li, ; Hailing Tang, ; Bangzhou Zhang,
| | - Hailing Tang
- Division of Gastroenterology, Xi’an Central Hospital, Xi’an, China
- *Correspondence: Yuantao Li, ; Hailing Tang, ; Bangzhou Zhang,
| | - Bangzhou Zhang
- Center for Research and Development, Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
- School of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- *Correspondence: Yuantao Li, ; Hailing Tang, ; Bangzhou Zhang,
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14
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Sanjeewani K, Lee KJ. Dietary Riboflavin Requirement of Pacific White Shrimp ( Litopenaeus vannamei). AQUACULTURE NUTRITION 2023; 2023:6685592. [PMID: 37143963 PMCID: PMC10154092 DOI: 10.1155/2023/6685592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/15/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023]
Abstract
This study was conducted to determine the dietary riboflavin requirement and its effects on growth performance, feed utilization, innate immunity, and diet digestibility of Litopenaeus vannamei. A riboflavin-free basal diet (R0) was formulated as a control, and six other diets were prepared by adding riboflavin of 10, 20, 30, 40, 50, and 60 mg/kg to the basal diet (designated as R10, R20, R30, R40, R50, and R60, respectively). Quadruplicate groups of shrimp (initial average weight 0.17 ± 0.00 g) were fed the diets six times a day for 8 weeks. Weight gain, specific growth rate, and protein efficiency ratio were significantly increased by riboflavin (p < 0.05). The maximum values were observed in shrimp fed R40 diet. The highest activities of phenoloxidase, nitro blue tetrazolium, superoxide dismutase, and glutathione peroxidase were observed in shrimp fed R40 diet. Lysozyme activity was significantly higher in shrimp fed R30 and R40 diets than that of shrimp fed R60 diet (p < 0.05). Intestinal villi were significantly longer in shrimp fed R50 and R60 diets compared to those of all other groups while the shortest villi were observed in R0 group (p < 0.05). Intestinal villi were clearly distinguished in shrimp fed higher levels of riboflavin compared to those of shrimp fed R0 and R10 diets. Apparent digestibility coefficients of dry matter and protein in diets were not significantly affected by riboflavin levels (p < 0.05). Whole-body proximate composition and hemolymph biochemical parameters were not significantly altered by dietary riboflavin (p < 0.05). Therefore, the results of this study indicate that riboflavin is essential to enhance growth performance, feed utilization, nonspecific immunity, and intestine morphology of shrimp. An optimal riboflavin requirement for the maximum growth of L. vannamei seems to be approximately 40.9 mg/kg diet.
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Affiliation(s)
- Kokila Sanjeewani
- Department of Marine Life Sciences, Jeju National University, Jeju 63243, Republic of Korea
| | - Kyeong-Jun Lee
- Department of Marine Life Sciences, Jeju National University, Jeju 63243, Republic of Korea
- Marine Science Institute, Jeju National University, Jeju 63333, Republic of Korea
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15
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Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution. Biometals 2022:10.1007/s10534-022-00480-8. [PMID: 36508064 PMCID: PMC10393863 DOI: 10.1007/s10534-022-00480-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
AbstractIron is important for bacterial growth and survival, as it is a common co-factor in essential enzymes. Although iron is very abundant in the earth crust, its bioavailability is low in most habitats because ferric iron is largely insoluble under aerobic conditions and at neutral pH. Consequently, bacteria have evolved a plethora of mechanisms to solubilize and acquire iron from environmental and host stocks. In this review, I focus on Pseudomonas spp. and first present the main iron uptake mechanisms of this taxa, which involve the direct uptake of ferrous iron via importers, the production of iron-chelating siderophores, the exploitation of siderophores produced by other microbial species, and the use of iron-chelating compounds produced by plants and animals. In the second part of this review, I elaborate on how these mechanisms affect interactions between bacteria in microbial communities, and between bacteria and their hosts. This is important because Pseudomonas spp. live in diverse communities and certain iron-uptake strategies might have evolved not only to acquire this essential nutrient, but also to gain relative advantages over competitors in the race for iron. Thus, an integrative understanding of the mechanisms of iron acquisition and the eco-evolutionary dynamics they drive at the community level might prove most useful to understand why Pseudomonas spp., in particular, and many other bacterial species, in general, have evolved such diverse iron uptake repertoires.
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16
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Mukti IJ, Sardari RRR, Kristjansdottir T, Hreggvidsson GO, Karlsson EN. Medium development and production of carotenoids and exopolysaccharides by the extremophile Rhodothermus marinus DSM16675 in glucose-based defined media. Microb Cell Fact 2022; 21:220. [PMID: 36274123 PMCID: PMC9590192 DOI: 10.1186/s12934-022-01946-7] [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: 07/19/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The marine thermophilic bacterium Rhodothermus marinus can degrade many polysaccharides which makes it interesting as a future cell factory. Progress using this bacterium has, however, been hampered by limited knowledge on media and conditions for biomass production, often resulting in low cell yields and low productivity, highlighting the need to develop conditions that allow studies of the microbe on molecular level. This study presents development of defined conditions that support growth, combined with evaluation of production of carotenoids and exopolysaccharides (EPSs) by R. marinus strain DSM 16675. RESULTS Two defined media were initially prepared: one including a low addition of yeast extract (modified Wolfe's medium) and one based on specific components (defined medium base, DMB) to which two amino acids (N and Q), were added. Cultivation trials of R. marinus DSM 16675 in shake flasks, resulted in maximum cell densities (OD620 nm) of 2.36 ± 0.057, cell dry weight (CDW) 1.2 ± 0.14 mg/L, total carotenoids 0.59 × 10-3 mg/L, and EPSs 1.72 ± 0.03 mg/L using 2 g/L glucose in DMB. In Wolfe's medium (supplemented by 0.05 g/L yeast extract and 2.5 g/L glucose), maximum OD620 nm was 2.07 ± 0.05, CDW 1.05 ± 0.07 mg/L, total carotenoids 0.39 × 10-3 mg/L, and EPSs 1.74 ± 0.2 mg/L. Growth trials at 5 g/L glucose in these media either failed or resulted in incomplete substrate utilization. To improve reproducibility and increase substrate utilization, a screening of macroelements (e.g. phosphate) in DMB, was combined with use of trace elements and vitamins of the modified Wolfe's medium. The resulting defined minimal R. marinus medium, (DRM), allowed reproducible cultivations to a final OD620nm of 6.6 ± 0.05, CDW 2.85 ± 0.07 mg/L, a maximum specific growth rate (µmax) of 0.26 h-1, total carotenoids 0.77 × 10-3 mg/L and EPSs 3.4 ± 0.17 mg/L in cultivations supplemented with up to 5 g/L glucose. CONCLUSION A minimal defined medium (DRM) was designed that resulted in reproducible growth and an almost doubled formation of both total carotenoids and EPSs. Such defined conditions, are necessary for systematic studies of metabolic pathways, to determine the specific requirements for growth and fully characterize metabolite production.
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Affiliation(s)
- Israt Jahan Mukti
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden
| | - Roya R R Sardari
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden.
| | - Thordis Kristjansdottir
- Matis Ohf, Vinlandsleid 12, 113, Reykjavik, Iceland.,Department of Biology, School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 102, Reykjavik, Iceland
| | - Gudmundur O Hreggvidsson
- Matis Ohf, Vinlandsleid 12, 113, Reykjavik, Iceland.,Department of Biology, School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 102, Reykjavik, Iceland
| | - Eva Nordberg Karlsson
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden
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17
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The performance of lactic acid bacteria in silage production: a review of modern biotechnology for silage improvement. Microbiol Res 2022; 266:127212. [DOI: 10.1016/j.micres.2022.127212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 11/23/2022]
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18
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Liu K, Abouelhassan Y, Zhang Y, Jin S, Huigens Iii RW. Transcript Profiling of Nitroxoline-Treated Biofilms Shows Rapid Up-regulation of Iron Acquisition Gene Clusters. ACS Infect Dis 2022; 8:1594-1605. [PMID: 35830188 PMCID: PMC10549994 DOI: 10.1021/acsinfecdis.2c00206] [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] [Indexed: 11/30/2022]
Abstract
Bacterial biofilms are surface-attached communities of slow- or non-replicating cells embedded within a protective matrix of biomolecules. Unlike free-floating planktonic bacteria, biofilms are innately tolerant to conventional antibiotics and are prevalent in recurring and chronic infections. Nitroxoline, a broad-spectrum biofilm-eradicating agent, was used to probe biofilm viability. Transcript profiling (RNA-seq) showed that 452 of 2594 genes (17.4%) in methicillin-resistant Staphylococcus aureus (MRSA) biofilms were differentially expressed after a 2 h treatment of nitroxoline. WoPPER analysis and time-course validation (RT-qPCR) revealed that gene clusters involved in iron acquisition (sbn, isd, MW2101, MW0695, fhu, and feo) were rapidly up-regulated following nitroxoline treatment, which is indicative of iron starvation in MRSA biofilms. In addition, genes related to oligopeptide transporters and riboflavin biosynthesis were found to be up-regulated, while genes related to carotenoid biosynthesis and nitrate assimilation were down-regulated. RT-qPCR experiments revealed that iron uptake transcripts were also up-regulated in established Staphylococcus epidermidis and Acinetobacter baumannii biofilms following nitroxoline treatment. Overall, we show RNA-seq to be an ideal platform to define cellular pathways critical for biofilm survival, in addition to demonstrating the need these bacterial communities have for iron.
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Affiliation(s)
- Ke Liu
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Yasmeen Abouelhassan
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research (ICBR), Gene Expression and Genotyping, University of Florida, Gainesville, Florida 32610, United States
| | - Shouguang Jin
- Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Robert W Huigens Iii
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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19
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Zhukova M, Sapountzis P, Schiøtt M, Boomsma JJ. Phylogenomic analysis and metabolic role reconstruction of mutualistic Rhizobiales hindgut symbionts of Acromyrmex leaf-cutting ants. FEMS Microbiol Ecol 2022; 98:6652133. [PMID: 35906195 DOI: 10.1093/femsec/fiac084] [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: 03/04/2022] [Revised: 07/03/2022] [Accepted: 07/27/2022] [Indexed: 11/12/2022] Open
Abstract
Rhizobiales are well-known plant-root nitrogen-fixing symbionts, but the functions of insect-associated Rhizobiales are poorly understood. We obtained genomes of three strains associated with Acromyrmex leaf-cutting ants and show that, in spite of being extracellular gut symbionts, they lost all pathways for essential amino acid biosynthesis, making them fully dependent on their hosts. Comparison with 54 Rhizobiales genomes showed that all insect-associated Rhizobiales lost the ability to fix nitrogen and that the Acromyrmex symbionts had exceptionally also lost the urease genes. However, the Acromyrmex strains share biosynthesis pathways for riboflavin vitamin, queuosine and a wide range of antioxidant enzymes likely to be beneficial for the ant fungus-farming symbiosis. We infer that the Rhizobiales symbionts catabolize excess of fungus-garden-derived arginine to urea, supplementing complementary Mollicutes symbionts that turn arginine into ammonia and infer that these combined symbiont activities stabilize the fungus-farming mutualism. Similar to the Mollicutes symbionts, the Rhizobiales species have fully functional CRISPR/Cas and R-M phage defenses, suggesting that these symbionts are important enough for the ant hosts to have precluded the evolution of metabolically cheaper defenseless strains.
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Affiliation(s)
- Mariya Zhukova
- Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Panagiotis Sapountzis
- Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
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20
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Wang C, Zhang J, Liu Q, Guo G, Huo W, Pei C, Xia C, Chen L, Zhang Y. Rumen protected riboflavin and rumen protected pantothenate improved growth performance, nutrient digestion and rumen fermentation in Angus bulls. Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Frenkel-Pinter M, Petrov AS, Matange K, Travisano M, Glass JB, Williams LD. Adaptation and Exaptation: From Small Molecules to Feathers. J Mol Evol 2022; 90:166-175. [PMID: 35246710 PMCID: PMC8975760 DOI: 10.1007/s00239-022-10049-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
Evolution works by adaptation and exaptation. At an organismal level, exaptation and adaptation are seen in the formation of organelles and the advent of multicellularity. At the sub-organismal level, molecular systems such as proteins and RNAs readily undergo adaptation and exaptation. Here we suggest that the concepts of adaptation and exaptation are universal, synergistic, and recursive and apply to small molecules such as metabolites, cofactors, and the building blocks of extant polymers. For example, adenosine has been extensively adapted and exapted throughout biological evolution. Chemical variants of adenosine that are products of adaptation include 2' deoxyadenosine in DNA and a wide array of modified forms in mRNAs, tRNAs, rRNAs, and viral RNAs. Adenosine and its variants have been extensively exapted for various functions, including informational polymers (RNA, DNA), energy storage (ATP), metabolism (e.g., coenzyme A), and signaling (cyclic AMP). According to Gould, Vrba, and Darwin, exaptation imposes a general constraint on interpretation of history and origins; because of exaptation, extant function should not be used to explain evolutionary history. While this notion is accepted in evolutionary biology, it can also guide the study of the chemical origins of life. We propose that (i) evolutionary theory is broadly applicable from the dawn of life to the present time from molecules to organisms, (ii) exaptation and adaptation were important and simultaneous processes, and (iii) robust origin of life models can be constructed without conflating extant utility with historical basis of origins.
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Affiliation(s)
- Moran Frenkel-Pinter
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA.,Institute of Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Anton S Petrov
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Kavita Matange
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Michael Travisano
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jennifer B Glass
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Loren Dean Williams
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA. .,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA. .,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA.
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22
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Effect of Lacticaseibacillus casei Zhang on iron status, immunity, and gut microbiota of mice fed with low-iron diet. J Funct Foods 2022. [DOI: 10.1016/j.jff.2021.104906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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23
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Abstract
Iron (Fe) plays important roles in both essential cellular processes and virulence pathways for many bacteria. Consequently, Fe withholding by the human innate immune system is an effective form of defense against bacterial infection. In this Perspective, we review recent studies that have established a foundation for our understanding of the impact of the metal-sequestering host defense protein calprotectin (CP) on bacterial Fe homeostasis. We also discuss two recently uncovered strategies for bacterial adaptation to Fe withholding by CP. Together, these studies provide insight into how Fe sequestration by CP affects bacterial pathogens that include Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus. Overall, recent studies suggest that Fe withholding by CP may have implications for bacterial survival and virulence in the host, and further explorations that directly address this possibility present an important area for discovery.
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Affiliation(s)
- Adunoluwa O. Obisesan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Emily M. Zygiel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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24
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Brandão A, Pires DP, Coppens L, Voet M, Lavigne R, Azeredo J. Differential transcription profiling of the phage LUZ19 infection process in different growth media. RNA Biol 2021; 18:1778-1790. [PMID: 33448239 PMCID: PMC8583145 DOI: 10.1080/15476286.2020.1870844] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022] Open
Abstract
RNA sequencing of phage-infected bacterial cultures offers a snapshot of transcriptional events occurring during the infection process, providing insights into the phage transcriptional organization as well as the bacterial response. To better mimic real environmental contexts, we performed RNA-seq of Pseudomonas aeruginosa PAO1 cultures infected with phage LUZ19 in a mammalian cell culture medium to better simulate a phage therapy event and the data were compared to lysogeny broth medium. Regardless of the media, phage LUZ19 induces significant transcriptional changes in the bacterial host over time, particularly during early infection (t = 5 min) and gradually shuts down bacterial transcription. In a common response in both media, 56 P. aeruginosa PAO1 genes are differentially transcribed and clustered into several functional categories such as metabolism, translation and transcription. Our data allowed us to tease apart a medium-specific response during infection from the identified infection-associated responses. This reinforces the concept that phages overtake bacterial transcriptome in a strict manner to gain control of the bacterial machinery and reallocate resources for infection, in this case overcoming the nutritional limitations of the mammalian cell culture medium. From a phage therapy perspective, this study contributes towards a better understanding of phage-host interaction in human physiological conditions and demonstrates the versatility of phage LUZ19 to adapt to different environments.
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Affiliation(s)
- Ana Brandão
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Diana P. Pires
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Lucas Coppens
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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25
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López-Pérez M, Jayakumar JM, Grant TA, Zaragoza-Solas A, Cabello-Yeves PJ, Almagro-Moreno S. Ecological diversification reveals routes of pathogen emergence in endemic Vibrio vulnificus populations. Proc Natl Acad Sci U S A 2021; 118:e2103470118. [PMID: 34593634 PMCID: PMC8501797 DOI: 10.1073/pnas.2103470118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Pathogen emergence is a complex phenomenon that, despite its public health relevance, remains poorly understood. Vibrio vulnificus, an emergent human pathogen, can cause a deadly septicaemia with over 50% mortality rate. To date, the ecological drivers that lead to the emergence of clinical strains and the unique genetic traits that allow these clones to colonize the human host remain mostly unknown. We recently surveyed a large estuary in eastern Florida, where outbreaks of the disease frequently occur, and found endemic populations of the bacterium. We established two sampling sites and observed strong correlations between location and pathogenic potential. One site is significantly enriched with strains that belong to one phylogenomic cluster (C1) in which the majority of clinical strains belong. Interestingly, strains isolated from this site exhibit phenotypic traits associated with clinical outcomes, whereas strains from the second site belong to a cluster that rarely causes disease in humans (C2). Analyses of C1 genomes indicate unique genetic markers in the form of clinical-associated alleles with a potential role in virulence. Finally, metagenomic and physicochemical analyses of the sampling sites indicate that this marked cluster distribution and genetic traits are strongly associated with distinct biotic and abiotic factors (e.g., salinity, nutrients, or biodiversity), revealing how ecosystems generate selective pressures that facilitate the emergence of specific strains with pathogenic potential in a population. This knowledge can be applied to assess the risk of pathogen emergence from environmental sources and integrated toward the development of novel strategies for the prevention of future outbreaks.
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Affiliation(s)
- Mario López-Pérez
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 Alicante, Spain
| | - Jane M Jayakumar
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
| | - Trudy-Ann Grant
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
| | - Asier Zaragoza-Solas
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 Alicante, Spain
| | - Pedro J Cabello-Yeves
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 Alicante, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816;
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
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26
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MdaB and NfrA, two novel reductases important in the survival and persistence of the major enteropathogen Campylobacter jejuni. J Bacteriol 2021; 204:e0042121. [PMID: 34606373 PMCID: PMC8765430 DOI: 10.1128/jb.00421-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The paralogues RrpA and RrpB, which are members of the MarR family of DNA binding proteins, are important for the survival of the global bacterial foodborne pathogen Campylobacter jejuni under redox stress. We report that RrpA is a positive regulator of mdaB, encoding a flavin-dependent quinone reductase that contributes to the protection from redox stress mediated by structurally diverse quinones, while RrpB negatively regulates the expression of cj1555c (renamed nfrA for NADPH-flavin reductase A), encoding a flavin reductase. NfrA reduces riboflavin at a greater rate than its derivatives, suggesting that exogenous free flavins are the natural substrate. MdaB and NfrA both prefer NADPH as an electron donor. Cysteine substitution and posttranslational modification analyses indicated that RrpA and RrpB employ a cysteine-based redox switch. Complete genome sequence analyses revealed that mdaB is frequently found in Campylobacter and related Helicobacter spp., while nfrA is predominant in C. jejuni strains. Quinones and flavins are redox cycling agents secreted by a wide range of cell types that can form damaging superoxide by one-electron reactions. We propose a model for stress adaptation where MdaB and NfrA facilitate a two-electron reduction mechanism to the less toxic hydroquinones, thus aiding survival and persistence of this major pathogen. IMPORTANCE Changes in cellular redox potential result in alteration in the oxidation state of intracellular metabolites and enzymes; consequently, cells make adjustments that favor growth and survival. The work we present here answers some of the many questions that have remained elusive over the years of investigation into the enigmatic microaerophile bacterium Campylobacter jejuni. We employed molecular approaches to understand the regulation mechanisms and functional analyses to reveal the roles of two novel quinone and flavin reductases; both serve as major pools of cellular redox-active molecules. This work extends our knowledge on bacterial redox sensing mechanisms and the significance of hemostasis.
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27
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Shafiee RT, Snow JT, Hester S, Zhang Q, Rickaby REM. Proteomic response of the marine ammonia-oxidising archaeon Nitrosopumilus maritimus to iron limitation reveals strategies to compensate for nutrient scarcity. Environ Microbiol 2021; 24:835-849. [PMID: 33876540 DOI: 10.1111/1462-2920.15491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/25/2021] [Indexed: 11/26/2022]
Abstract
Dissolved iron (Fe) is vanishingly low in the oceans, with ecological success conferred to microorganisms that can restructure their biochemistry to maintain high growth rates during Fe scarcity. Chemolithoautotrophic ammonia-oxidising archaea (AOA) are highly abundant in the oceans, constituting ~30% of cells below the photic zone. Here we examine the proteomic response of the AOA isolate Nitrosopumilus maritimus to growth-limiting Fe concentrations. Under Fe limitation, we observed a significant reduction in the intensity of Fe-dense ferredoxins associated with respiratory complex I whilst complex III and IV proteins with more central roles in the electron transport chain remain unchanged. We concomitantly observed an increase in the intensity of Fe-free functional alternatives such as flavodoxin and plastocyanin, thioredoxin and alkyl hydroperoxide which are known to mediate electron transport and reactive oxygen species detoxification, respectively. Under Fe limitation, we found a marked increase in the intensity of the ABC phosphonate transport system (Phn), highlighting an intriguing link between Fe and P cycling in N. maritimus. We hypothesise that an elevated uptake of exogenous phosphonates under Fe limitation may either supplement N. maritimus' endogenous methylphosphonate biosynthesis pathway - which requires Fe - or enhance the production of phosphonate-containing exopolysaccharides known to efficiently bind environmental Fe.
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Affiliation(s)
- Roxana T Shafiee
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
| | - Joseph T Snow
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
| | - Svenja Hester
- Department of Biochemistry, South Parks Road, University of Oxford, Oxfordshire, OX1 3QU, UK
| | - Qiong Zhang
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
| | - Rosalind E M Rickaby
- Department of Earth Sciences, South Parks Road, University of Oxford, Oxfordshire, OX1 3AN, UK
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28
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Currin-Ross D, Husdell L, Pierens GK, Mok NE, O'Neill SL, Schirra HJ, Brownlie JC. The Metabolic Response to Infection With Wolbachia Implicates the Insulin/Insulin-Like-Growth Factor and Hypoxia Signaling Pathways in Drosophila melanogaster. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.623561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The endosymbiotic bacteria, Wolbachia, are best known for their ability to manipulate insect-host reproduction systems that enhance their vertical transmission within host populations. Increasingly, Wolbachia have been shown to depend on their hosts' metabolism for survival and in turn provision metabolites to their host. Wolbachia depends completely on the host for iron and as such iron has been speculated to be a fundamental aspect of Wolbachia-host interplay. However, the mechanisms by which dietary iron levels, Wolbachia, and its host interact remain to be elucidated. To understand the metabolic dependence of Wolbachia on its host, the possibility of metabolic provisioning and extraction, and the interplay with available dietary iron, we have used NMR-based metabolomics and compared metabolite profiles of Wolbachia-infected and uninfected Drosophila melanogaster flies raised on varying levels of dietary iron. We observed marked metabolite differences in the affected metabolite pathways between Wolbachia-infected and uninfected Drosophila, which were dependent on the dietary iron levels. Excess iron led to lipid accumulation, whereas iron deficiency led to changes in carbohydrate levels. This represents a major metabolic shift triggered by alterations in iron levels. Lipids, some amino acids, carboxylic acids, and nucleosides were the major metabolites altered by infection. The metabolic response to infection showed a reprogramming of the mitochondrial metabolism in the host. Based on these observations, we developed a physiological model which postulates that the host's insulin/insulin-like-growth factor pathway is depressed and the hypoxia signaling pathway is activated upon Wolbachia infection. This reprogramming leads to predominantly non-oxidative metabolism in the host, whereas Wolbachia maintains oxidative metabolism. Our data also support earlier predictions of the extraction of alanine from the host while provisioning riboflavin and ATP to the host.
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29
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Augmentation of the Riboflavin-Biosynthetic Pathway Enhances Mucosa-Associated Invariant T (MAIT) Cell Activation and Diminishes Mycobacterium tuberculosis Virulence. mBio 2021; 13:e0386521. [PMID: 35164552 PMCID: PMC8844931 DOI: 10.1128/mbio.03865-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mucosa-associated invariant T (MAIT) cells play a critical role in antimicrobial defense. Despite increased understanding of their mycobacterial ligands and the clinical association of MAIT cells with tuberculosis (TB), their function in protection against Mycobacterium tuberculosis infection remains unclear. Here, we show that overexpressing key genes of the riboflavin-biosynthetic pathway potentiates MAIT cell activation and results in attenuation of M. tuberculosis virulence in vivo. Further, we observed greater control of M. tuberculosis infection in MAIThi CAST/EiJ mice than in MAITlo C57BL/6J mice, highlighting the protective role of MAIT cells against TB. We also endogenously adjuvanted Mycobacterium bovis BCG with MR1 ligands via overexpression of the lumazine synthase gene ribH and evaluated its protective efficacy in the mouse model of M. tuberculosis infection. Altogether, our findings demonstrate that MAIT cells confer host protection against TB and that overexpression of genes in the riboflavin-biosynthetic pathway attenuates M. tuberculosis virulence. Enhancing MAIT cell-mediated immunity may also offer a novel approach toward improved vaccines against TB. IMPORTANCE Mucosa-associated invariant T (MAIT) cells are an important subset of innate lymphocytes that recognize microbial ligands derived from the riboflavin biosynthesis pathway and mediate antimicrobial immune responses. Modulated MAIT cell responses have been noted in different forms of tuberculosis. However, it has been unclear if increased MAIT cell abundance is protective against TB disease. In this study, we show that augmentation of the mycobacterial MAIT cell ligands leads to higher MAIT cell activation with reduced M. tuberculosis virulence and that elevated MAIT cell abundance confers greater control of M. tuberculosis infection. Our study also highlights the potential of endogenously adjuvanting the traditional BCG vaccine with MR1 ligands to augment MAIT cell activation. This study increases current knowledge on the roles of the riboflavin-biosynthetic pathway and MAIT cell activation in M. tuberculosis virulence and host immunity against TB.
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30
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Sun B, Xue Y, Du X, He X, Zou Z, Tian X, Hu Z, Liu H, Islam N, Hu Q. Identification of genetic determinants of hemolytic activity of Riemerella anatipestifer using random transposon mutagenesis. Vet Res 2021; 52:19. [PMID: 33579370 PMCID: PMC7881567 DOI: 10.1186/s13567-021-00900-6] [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: 09/30/2020] [Accepted: 01/16/2021] [Indexed: 11/18/2022] Open
Abstract
Riemerella anatipestifer causes epizootic infectious disease in poultry resulting in serious economic losses especially to the duck industry. In our previous study, R. anatipestifer was found to lyse duck erythrocytes in vitro. In the present study, a random Tn4351 mutagenesis library of hemolytic R. anatipestifer strain SX containing 4000 mutants was constructed to investigate the genetic basis of hemolytic activity. Thirty mutants with reduced hemolytic activity and one with increased hemolytic activity were screened and insertions in 24 genes were identified. Of these genes, four were predicted to encode outer membrane proteins, one encoded a cytoplasmic membrane protein, 11 encoded cytoplasmic proteins, and eight encoded proteins with unknown locations. Based on current annotations of the R. anatipestifer genomes, of the 24 genes, 7 (29.17%) were involved in iron utilization. The hemolytic activities of the complemented strains M2 (pRES-Riean_0790) and M18 (pRES-Riean_0653) were restored, indicating that both Riean_0653 and Riean_0790 are involved in the hemolytic activity of strain SX. However, the recombinant proteins rRiean_0317, rRiean_0790, rRiean_0653, rRiean_1027, rRiean_1143, and rRiean_1561 had no hemolytic activity, suggesting that none were hemolysins.
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Affiliation(s)
- Bingqing Sun
- Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, 200241, China.,Shanghai Animal Disease Control Center, 30 Lane 855 Hongjing Road, Shanghai, 201103, China
| | - Yafei Xue
- Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, 200241, China
| | - Xiaoli Du
- Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, 200241, China
| | - Xiaohua He
- Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, 200241, China
| | - Zuocheng Zou
- Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, 200241, China
| | - Xiangqiang Tian
- Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, 200241, China
| | - Zhonghao Hu
- Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, 200241, China
| | - Haoyang Liu
- Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, 200241, China
| | - Nazrul Islam
- Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, 200241, China
| | - Qinghai Hu
- Shanghai Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Shanghai, 200241, China.
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31
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Gheshlaghi Z, Luis-Villarroya A, Álvarez-Fernández A, Khorassani R, Abadía J. Iron deficient Medicago scutellata grown in nutrient solution at high pH accumulates and secretes large amounts of flavins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110664. [PMID: 33487332 DOI: 10.1016/j.plantsci.2020.110664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 06/12/2023]
Abstract
Flavin synthesis and secretion is an integral part of the toolbox of root-borne Fe facilitators used by Strategy I species upon Fe deficiency. The Fe-deficiency responses of the wild legume Medicago scutellata grown in nutrient solution have been studied at two different pH values (5.5 and 7.5). Parameters studied include leaf chlorophyll, nutrient solution pH, concentrations and contents of micronutrients, flavin accumulation in roots, flavin export to the medium, and root ferric chelate reductase and acidification activities. Results show that M. scutellata behaves upon Fe deficiency as a Strategy I species, with a marked capacity for synthesizing flavins (riboflavin and three hydroxylated riboflavin derivatives), which becomes more intense at high pH. Results also show that this species is capable of exporting a large amount of flavins to the external medium, both at pH 5.5 and 7.5. This is the first report of a species having a major flavin secretion at pH 7.5, in contrast with the very low flavin secretion found in other flavin-producing species such as Beta vulgaris and M. truncatula. These results provide further support to the hypothesis that flavin secretion is relevant for Fe acquisition at high pH, and open the possibility to improve the Fe-efficiency responses in legumes of agronomic interest.
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Affiliation(s)
- Zahra Gheshlaghi
- Department of Soil Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, 9177948974, Iran.
| | - Adrián Luis-Villarroya
- Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Av. Montañana 1005, E-50059, Zaragoza, Spain.
| | - Ana Álvarez-Fernández
- Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Av. Montañana 1005, E-50059, Zaragoza, Spain.
| | - Reza Khorassani
- Department of Soil Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, 9177948974, Iran.
| | - Javier Abadía
- Department of Plant Nutrition, Aula Dei Experimental Station, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Av. Montañana 1005, E-50059, Zaragoza, Spain.
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32
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Kundra P, Rachmühl C, Lacroix C, Geirnaert A. Role of Dietary Micronutrients on Gut Microbial Dysbiosis and Modulation in Inflammatory Bowel Disease. Mol Nutr Food Res 2021. [DOI: 10.1002/mnfr.201901271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Palni Kundra
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Carole Rachmühl
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
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33
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Dauros-Singorenko P, Wiles S, Swift S. Staphylococcus aureus Biofilms and Their Response to a Relevant in vivo Iron Source. Front Microbiol 2020; 11:509525. [PMID: 33408695 PMCID: PMC7779473 DOI: 10.3389/fmicb.2020.509525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 11/23/2020] [Indexed: 11/29/2022] Open
Abstract
Biofilm infections can be chronic, life threatening and challenging to eradicate. Understanding in vivo stimuli affecting the biofilm cycle is one step toward targeted prevention strategies. Iron restriction by the host is a stimulus for biofilm formation for some Staphylococcus aureus isolates; however, in some infection scenarios bacteria are exposed to abundant amounts of hemoglobin (Hb), which S. aureus is able to use as iron source. Thus, we hypothesized a role for Hb in the biofilm infection. Microplate “biofilm” assays showed biofilm-matrix production was increased in the presence of hemoglobin when compared to the provision of iron as an inorganic salt. Microscopic analysis of biofilms showed that the provision of iron as hemoglobin consistently caused thicker and more structured biofilms when compared to the effect of the inorganic iron source. Iron responsive biofilm gene expression analysis showed that Agr Quorum Sensing, a known biofilm dispersal marker, was repressed with hemoglobin but induced with an equivalent amount of inorganic iron in the laboratory strain Newman. The gene expression of two biofilm structuring agents, PSMα and PSMβ, differed in the response to the iron source provided and was not correlated to hemoglobin-structured biofilms. A comparison of the model pathogen S. aureus Newman with local clinical isolates demonstrated that while there was a similar phenotypic biofilm response to hemoglobin, there was substantial variation in the expression of key biofilm dispersal markers, suggesting an underappreciated variation in biofilm regulome among S. aureus isolates and that no general inferences can be made by studying the behavior of single strains.
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Affiliation(s)
- Priscila Dauros-Singorenko
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Siouxsie Wiles
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
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34
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Averianova LA, Balabanova LA, Son OM, Podvolotskaya AB, Tekutyeva LA. Production of Vitamin B2 (Riboflavin) by Microorganisms: An Overview. Front Bioeng Biotechnol 2020; 8:570828. [PMID: 33304888 PMCID: PMC7693651 DOI: 10.3389/fbioe.2020.570828] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
Riboflavin is a crucial micronutrient that is a precursor to coenzymes flavin mononucleotide and flavin adenine dinucleotide, and it is required for biochemical reactions in all living cells. For decades, one of the most important applications of riboflavin has been its global use as an animal and human nutritional supplement. Being well-informed of the latest research on riboflavin production via the fermentation process is necessary for the development of new and improved microbial strains using biotechnology and metabolic engineering techniques to increase vitamin B2 yield. In this review, we describe well-known industrial microbial producers, namely, Ashbya gossypii, Bacillus subtilis, and Candida spp. and summarize their biosynthetic pathway optimizations through genetic and metabolic engineering, combined with random chemical mutagenesis and rational medium components to increase riboflavin production.
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Affiliation(s)
- Liudmila A. Averianova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, Vladivostok, Russia
| | - Larissa A. Balabanova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, Vladivostok, Russia
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Oksana M. Son
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, Vladivostok, Russia
- ARNIKA, Territory of PDA Nadezhdinskaya, Primorsky Krai, Russia
| | - Anna B. Podvolotskaya
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, Vladivostok, Russia
- ARNIKA, Territory of PDA Nadezhdinskaya, Primorsky Krai, Russia
| | - Liudmila A. Tekutyeva
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, Vladivostok, Russia
- ARNIKA, Territory of PDA Nadezhdinskaya, Primorsky Krai, Russia
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35
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IurV, Encoded by ORF VCA0231, Is Involved in the Regulation of Iron Uptake Genes in Vibrio cholerae. Genes (Basel) 2020; 11:genes11101184. [PMID: 33053678 PMCID: PMC7600106 DOI: 10.3390/genes11101184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022] Open
Abstract
The pathogen Vibrio cholerae has multiple iron acquisition systems which allow bacteria to exploit a variety of iron sources across the different environments on which it thrives. The expression of such iron uptake systems is highly regulated, mainly by the master iron homeostasis regulator Fur but also by other mechanisms. Recently, we documented that the expression of many of the iron-responsive genes is also modulated by riboflavin. Among them, the open reading frame VCA0231, repressed both by riboflavin and iron, encodes a putative transcriptional regulator of the AraC/XylS family. Nonetheless, the genes or functions affected by this factor are unknown. In the present study, a series of in silico analyses was performed in order to identify the putative functions associated with the product of VCA0231. The STRING database predicted many iron uptake genes as functional partners for the product of VCA0231. In addition, a genomic neighborhood analysis with the Enzyme Function Initiative tools detected many Pfam families involved in iron homeostasis genetically associated with VCA0231. Moreover, a phylogenetic tree showed that other AraC/XylS members known to regulate siderophore utilization in bacteria clustered together and the product of VCA0231 localized in this cluster. This suggested that the product of VCA0231, here named IurV, is involved in the regulation of iron uptake processes. RNAseq was performed to determine the transcriptional effects of a deletion in VCA0231. A total of 52 genes were overexpressed and 21 genes were downregulated in response to the iurV deletion. Among these, several iron uptake genes and other iron homeostasis-related genes were found. Six gene ontology (GO) functional terms were enriched in the upregulated genes, of which five were related to iron metabolism. The regulatory pattern observed in the transcriptomics of a subset of genes was independently confirmed by quantitative real time PCR analysis. The results indicate that IurV is a novel regulator of the AraC/XylS family involved in the repression of iron uptake genes. Whether this effect is direct or indirect remains to be determined.
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Lozano Aguirre LF, Salazar JC, Vásquez JI, García-Angulo VA. Interdependency of regulatory effects of iron and riboflavin in the foodborne pathogen Shigella flexneri determined by integral transcriptomics. PeerJ 2020; 8:e9553. [PMID: 32983629 PMCID: PMC7500357 DOI: 10.7717/peerj.9553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/24/2020] [Indexed: 11/24/2022] Open
Abstract
Shigella flexneri is the causative agent of dysentery. For pathogens, iron is a critical micronutrient as its bioavailability is usually low in bacterial niches. This metal is involved in critical physiological processes mainly as a component of important metabolic molecules involved in redox reactions. Usually bacteria respond to fluctuations in iron availability to regulate iron acquisition and other iron-related functions. Recently the close metabolic feedback between iron and riboflavin, another pivotal biological redox agent, began to draw attention in bacteria. This is a widespread biological phenomenon, partly characterized by the coordination of regulatory responses to iron and riboflavin, probably owed to the involvement of these cofactors in common processes. Nonetheless, no systematic analyses to determine the extent of this regulatory effect have been performed in any species. Here, the transcriptomics responses to iron, riboflavin, iron in the presence of riboflavin and riboflavin in the presence of iron were assessed and compared in S. flexneri. The riboflavin regulon had a 43% overlap with the iron regulon. Notably, the presence of riboflavin highly increased the number of iron-responsive genes. Reciprocally, iron drastically changed the pool of riboflavin-responsive genes. Gene ontology (GO) functional terms enrichment analysis showed that biological processes were distinctively enriched for each subgroup of responsive genes. Among the biological processes regulated by iron and riboflavin were iron uptake, amino acids metabolism and electron transfer for ATP synthesis. Thus, iron and riboflavin highly affect the transcriptomics responses induced by each other in S. flexneri. GO terms analysis suggests that iron and riboflavin coordinately regulate specific physiological functions involving redox metabolism.
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Affiliation(s)
- Luis Fernando Lozano Aguirre
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Juan Carlos Salazar
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - José Ignacio Vásquez
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John, Canada
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Zhang Y, Sen S, Giedroc DP. Iron Acquisition by Bacterial Pathogens: Beyond Tris-Catecholate Complexes. Chembiochem 2020; 21:1955-1967. [PMID: 32180318 PMCID: PMC7367709 DOI: 10.1002/cbic.201900778] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/06/2020] [Indexed: 12/11/2022]
Abstract
Sequestration of the essential nutrient iron from bacterial invaders that colonize the vertebrate host is a central feature of nutritional immunity and the "fight over transition metals" at the host-pathogen interface. The iron quota for many bacterial pathogens is large, as iron enzymes often make up a significant share of the metalloproteome. Iron enzymes play critical roles in respiration, energy metabolism, and other cellular processes by catalyzing a wide range of oxidation-reduction, electron transfer, and oxygen activation reactions. In this Concept article, we discuss recent insights into the diverse ways that bacterial pathogens acquire this essential nutrient, beyond the well-characterized tris-catecholate FeIII complexes, in competition and cooperation with significant host efforts to cripple these processes. We also discuss pathogen strategies to adapt their metabolism to less-than-optimal iron concentrations, and briefly speculate on what might be an integrated adaptive response to the concurrent limitation of both iron and zinc in the infected host.
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Affiliation(s)
- Yifan Zhang
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Sambuddha Sen
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
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Levade I, Saber MM, Midani FS, Chowdhury F, Khan AI, Begum YA, Ryan ET, David LA, Calderwood SB, Harris JB, LaRocque RC, Qadri F, Shapiro BJ, Weil AA. Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study. J Infect Dis 2020; 223:342-351. [PMID: 32610345 PMCID: PMC7857355 DOI: 10.1093/infdis/jiaa358] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Susceptibility to Vibrio cholerae infection is affected by blood group, age, and preexisting immunity, but these factors only partially explain who becomes infected. A recent study used 16S ribosomal RNA amplicon sequencing to quantify the composition of the gut microbiome and identify predictive biomarkers of infection with limited taxonomic resolution. METHODS To achieve increased resolution of gut microbial factors associated with V. cholerae susceptibility and identify predictors of symptomatic disease, we applied deep shotgun metagenomic sequencing to a cohort of household contacts of patients with cholera. RESULTS Using machine learning, we resolved species, strains, gene families, and cellular pathways in the microbiome at the time of exposure to V. cholerae to identify markers that predict infection and symptoms. Use of metagenomic features improved the precision and accuracy of prediction relative to 16S sequencing. We also predicted disease severity, although with greater uncertainty than our infection prediction. Species within the genera Prevotella and Bifidobacterium predicted protection from infection, and genes involved in iron metabolism were also correlated with protection. CONCLUSION Our results highlight the power of metagenomics to predict disease outcomes and suggest specific species and genes for experimental testing to investigate mechanisms of microbiome-related protection from cholera.
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Affiliation(s)
- Inès Levade
- Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Morteza M Saber
- Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada
| | - Firas S Midani
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, USA,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Fahima Chowdhury
- Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Ashraful I Khan
- Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Yasmin A Begum
- Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lawrence A David
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina, USA,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA,Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Stephen B Calderwood
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA,Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason B Harris
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Regina C LaRocque
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Firdausi Qadri
- Center for Vaccine Sciences, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - B Jesse Shapiro
- Department of Biological Sciences, University of Montreal, Montreal, Quebec, Canada,Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada,McGill Genome Centre, Montreal, Quebec, Canada,Correspondence: B. Jesse Shapiro, McGill University, Montreal, Quebec, Canada ()
| | - Ana A Weil
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
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Abstract
Exoelectrogens are able to transfer electrons extracellularly, enabling them to respire on insoluble terminal electron acceptors. Extensively studied exoelectrogens, such as Geobacter sulfurreducens and Shewanella oneidensis, are Gram negative. More recently, it has been reported that Gram-positive bacteria, such as Listeria monocytogenes and Enterococcus faecalis, also exhibit the ability to transfer electrons extracellularly, although it is still unclear whether this has a function in respiration or in redox control of the environment, for instance, by reducing ferric iron for iron uptake. In this issue of Journal of Bacteriology, Hederstedt and colleagues report on experiments that directly compare extracellular electron transfer (EET) pathways for ferric iron reduction and respiration and find a clear difference (L. Hederstedt, L. Gorton, and G. Pankratova, J Bacteriol 202:e00725-19, 2020, https://doi.org/10.1128/JB.00725-19), providing further insights and new questions into the function and metabolic pathways of EET in Gram-positive bacteria.
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Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1. Sci Rep 2020; 10:3787. [PMID: 32123183 PMCID: PMC7051946 DOI: 10.1038/s41598-020-59731-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023] Open
Abstract
Transcription is of the most crucial steps of gene expression in bacteria, whose regulation guarantees the bacteria's ability to adapt to varying environmental conditions. Discovering the molecular basis and genomic principles of the transcriptional regulation is thus one of the most important tasks in cellular and molecular biology. Here, a comprehensive phylogenetic footprinting framework was implemented to predict maximal regulons of Lactococcus lactis subsp. lactis IO-1, a lactic acid bacterium known for its high potentials in nisin Z production as well as efficient xylose consumption which have made it a promising biotechnological strain. A total set of 321 regulons covering more than 90% of all the bacterium's operons have been elucidated and validated according to available data. Multiple novel biologically-relevant members were introduced amongst which arsC, mtlA and mtl operon for BusR, MtlR and XylR regulons can be named, respectively. Moreover, the effect of riboflavin on nisin biosynthesis was assessed in vitro and a negative correlation was observed. It is believed that understandings from such networks not only can be useful for studying transcriptional regulatory potentials of the target organism but also can be implemented in biotechnology to rationally design favorable production conditions.
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Morici P, Battisti A, Tortora G, Menciassi A, Checcucci G, Ghetti F, Sgarbossa A. The in vitro Photoinactivation of Helicobacter pylori by a Novel LED-Based Device. Front Microbiol 2020; 11:283. [PMID: 32153551 PMCID: PMC7047934 DOI: 10.3389/fmicb.2020.00283] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/07/2020] [Indexed: 12/22/2022] Open
Abstract
The rise of antibiotic resistance is the main cause for the failure of conventional antibiotic therapy of Helicobacter pylori infection, which is often associated with severe gastric diseases, including gastric cancer. In the last years, alternative non-pharmacological approaches have been considered in the treatment of H. pylori infection. Among these, antimicrobial PhotoDynamic Therapy (aPDT), a light-based treatment able to photoinactivate a wide range of bacteria, viruses, fungal and protozoan parasites, could represent a promising therapeutic strategy. In the case of H. pylori, aPDT can exploit photoactive endogenous porphyrins, such as protoporphyrin IX and coproporphyrin I and III, to induce photokilling, without any other exogenous photosensitizers. With the aim of developing an ingestible LED-based robotic pill for minimally invasive intragastric treatment of H. pylori infection, it is crucial to determine the best illumination parameters to activate the endogenous photosensitizers. In this study the photokilling effect on H. pylori has been evaluated by using a novel LED-based device, designed for testing the appropriate LEDs for the pill and suitable to perform in vitro irradiation experiments. Exposure to visible light induced bacterial photokilling most effectively at 405 nm and 460 nm. Sub-lethal light dose at 405 nm caused morphological changes on bacterial surface indicating the cell wall as one of the main targets of photodamage. For the first time endogenous photosensitizing molecules other than porphyrins, such as flavins, have been suggested to be involved in the 460 nm H. pylori photoinactivation.
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Affiliation(s)
- Paola Morici
- Nanoscience Institute, CNR and NEST, Scuola Normale Superiore, Pisa, Italy
| | - Antonella Battisti
- Nanoscience Institute, CNR and NEST, Scuola Normale Superiore, Pisa, Italy
| | - Giuseppe Tortora
- The BioRobotics Institute, Polo Sant'Anna Valdera, Scuola Superiore Sant'Anna, Pontedera, Italy
| | - Arianna Menciassi
- The BioRobotics Institute, Polo Sant'Anna Valdera, Scuola Superiore Sant'Anna, Pontedera, Italy
| | - Giovanni Checcucci
- Nanoscience Institute, CNR and NEST, Scuola Normale Superiore, Pisa, Italy
| | - Francesco Ghetti
- Nanoscience Institute, CNR and NEST, Scuola Normale Superiore, Pisa, Italy
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Abstract
Calprotectin (CP) is a versatile player in the metal-withholding innate immune response, a process termed "nutritional immunity." CP is a heterooligomer of the polypeptides S100A8 and S100A9 and houses two transition-metal-binding sites at its S100A8/S100A9 heterodimer interface. During infection, CP is released from host cells and sequesters "bioavailable" transition metal ions in the extracellular space, thereby preventing microbial acquisition of these essential nutrients. For many years, the role of CP in nutritional immunity was interpreted in the contexts of Mn(II) and Zn(II) limitation, but recent work has broadened our understanding of its contributions to this process. We uncovered that CP provides a form of nutritional immunity that has previously received little attention: the battle between host and microbe for ferrous iron (Fe(II)). In this Account, we present our current understanding of Fe(II) coordination by CP and its role in Fe(II) withholding as well as considerations for future discovery. Nutritional immunity was first described in the context of host-microbe competition for ferric iron (Fe(III)). The battle for Fe(II) has received comparably little attention because the abundance of Fe(II) at infection sites and the importance of Fe(II) acquisition for microbial pathogenesis were recognized only recently. Several years ago, we discovered that human CP sequesters Fe(II) at its His6 site with subpicomolar affinity and thus hypothesized that it provides a means for Fe(II) limitation by the host during microbial infection. Fe(II) coordination by CP is unprecedented in biology because of its novel hexahistidine coordination sphere and its high-affinity binding, which surpasses that of other known Fe(II)-binding proteins. CP is also capable of shifting the Fe redox equilibrium by stabilizing Fe(II) in aerobic solution and can thereby sequester Fe in both reducing and nonreducing environments. These coordination chemistry studies allowed us to hypothesize that CP provides a means for Fe(II) limitation by the host during microbial infection. While investigating this putative Fe(II)-sequestering function, we discovered that CP withholds Fe from diverse bacterial pathogens. Recent studies by our lab and others of the bacterial pathogens Pseudomonas aeruginosa and Acinetobacter baumannii have shown that, by preventing sufficient Fe acquisition, CP induces Fe starvation responses in these organisms. As a result, CP affects bacterial virulence and metabolism. We also elucidated a complex interplay between CP and secondary metabolites produced by P. aeruginosa during the competition for Fe. Our work provides a foundation for understanding how CP affects Fe homeostasis during microbial infection. We believe that understanding how bacterial physiology is altered when challenged with Fe(II) withholding by CP will likely reveal crucial determinants of bacterial survival within the host.
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Affiliation(s)
- Emily M. Zygiel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Wang J, Lonergan ZR, Gonzalez-Gutierrez G, Nairn BL, Maxwell CN, Zhang Y, Andreini C, Karty JA, Chazin WJ, Trinidad JC, Skaar EP, Giedroc DP. Multi-metal Restriction by Calprotectin Impacts De Novo Flavin Biosynthesis in Acinetobacter baumannii. Cell Chem Biol 2019; 26:745-755.e7. [PMID: 30905682 PMCID: PMC6525019 DOI: 10.1016/j.chembiol.2019.02.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/20/2019] [Accepted: 02/18/2019] [Indexed: 02/07/2023]
Abstract
Calprotectin (CP) inhibits bacterial viability through extracellular chelation of transition metals. However, how CP influences general metabolism remains largely unexplored. We show here that CP restricts bioavailable Zn and Fe to the pathogen Acinetobacter baumannii, inducing an extensive multi-metal perturbation of cellular physiology. Proteomics reveals severe metal starvation, and a strain lacking the candidate ZnII metallochaperone ZigA possesses altered cellular abundance of multiple essential Zn-dependent enzymes and enzymes in de novo flavin biosynthesis. The ΔzigA strain exhibits decreased cellular flavin levels during metal starvation. Flavin mononucleotide provides regulation of this biosynthesis pathway, via a 3,4-dihydroxy-2-butanone 4-phosphate synthase (RibB) fusion protein, RibBX, and authentic RibB. We propose that RibBX ensures flavin sufficiency under CP-induced Fe limitation, allowing flavodoxins to substitute for Fe-ferredoxins as cell reductants. These studies elucidate adaptation to nutritional immunity and define an intersection between metallostasis and cellular metabolism in A. baumannii.
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Affiliation(s)
- Jiefei Wang
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Zachery R Lonergan
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Brittany L Nairn
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christina N Maxwell
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Yixiang Zhang
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Laboratory for Biological Mass Spectrometry, Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Claudia Andreini
- Magnetic Resonance Centre (CERM), University of Florence, Florence, 50019 Sesto Fiorentino, Italy
| | - Jonathan A Karty
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Walter J Chazin
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Laboratory for Biological Mass Spectrometry, Department of Chemistry, Indiana University, Bloomington, IN 47405, USA.
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
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