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Singh S, Gola C, Singh B, Agrawal V, Chaba R. D-galactonate metabolism in enteric bacteria: a molecular and physiological perspective. Curr Opin Microbiol 2024; 81:102524. [PMID: 39137493 DOI: 10.1016/j.mib.2024.102524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024]
Abstract
D-galactonate, a widely prevalent sugar acid, was first reported as a nutrient source for enteric bacteria in the 1970s. Since then, decades of research enabled a description of the modified Entner-Doudoroff pathway involved in its degradation and reported the structural and biochemical features of its metabolic enzymes, primarily in Escherichia coli K-12. However, only in the last few years, the D-galactonate transporter has been characterized, and the regulation of the dgo operon, encoding the structural genes for the transporter and enzymes of D-galactonate metabolism, has been detailed. Notably, in recent years, multiple evolutionary studies have identified the dgo operon as a dominant target for adaptation of E. coli in the mammalian gut. Despite considerable research on dgo operon, numerous fundamental questions remain to be addressed. The emerging relevance of the dgo operon in host-bacterial interactions further necessitates the study of D-galactonate metabolism in other enterobacterial strains.
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Affiliation(s)
- Swati Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Chetna Gola
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Bhupinder Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Vishal Agrawal
- Amity School of Biological Sciences, Amity University Punjab, Mohali, SAS Nagar, Punjab 140306, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India.
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2
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Huening KA, Groves JT, Wildenthal JA, Tabita FR, North JA. Escherichia coli possessing the dihydroxyacetone phosphate shunt utilize 5'-deoxynucleosides for growth. Microbiol Spectr 2024; 12:e0308623. [PMID: 38441472 PMCID: PMC10986504 DOI: 10.1128/spectrum.03086-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 02/17/2024] [Indexed: 03/08/2024] Open
Abstract
All organisms utilize S-adenosyl-l-methionine (SAM) as a key co-substrate for the methylation of biological molecules, the synthesis of polyamines, and radical SAM reactions. When these processes occur, 5'-deoxy-nucleosides are formed as byproducts such as S-adenosyl-l-homocysteine, 5'-methylthioadenosine (MTA), and 5'-deoxyadenosine (5dAdo). A prevalent pathway found in bacteria for the metabolism of MTA and 5dAdo is the dihydroxyacetone phosphate (DHAP) shunt, which converts these compounds into dihydroxyacetone phosphate and 2-methylthioacetaldehyde or acetaldehyde, respectively. Previous work in other organisms has shown that the DHAP shunt can enable methionine synthesis from MTA or serve as an MTA and 5dAdo detoxification pathway. Rather, the DHAP shunt in Escherichia coli ATCC 25922, when introduced into E. coli K-12, enables the use of 5dAdo and MTA as a carbon source for growth. When MTA is the substrate, the sulfur component is not significantly recycled back to methionine but rather accumulates as 2-methylthioethanol, which is slowly oxidized non-enzymatically under aerobic conditions. The DHAP shunt in ATCC 25922 is active under oxic and anoxic conditions. Growth using 5-deoxy-d-ribose was observed during aerobic respiration and anaerobic respiration with Trimethylamine N-oxide (TMAO), but not during fermentation or respiration with nitrate. This suggests the DHAP shunt may only be relevant for extraintestinal pathogenic E. coli lineages with the DHAP shunt that inhabit oxic or TMAO-rich extraintestinal environments. This reveals a heretofore overlooked role of the DHAP shunt in carbon and energy metabolism from ubiquitous SAM utilization byproducts and suggests a similar role may occur in other pathogenic and non-pathogenic bacteria with the DHAP shunt. IMPORTANCE The acquisition and utilization of organic compounds that serve as growth substrates are essential for Escherichia coli to grow and multiply. Ubiquitous enzymatic reactions involving S-adenosyl-l-methionine as a co-substrate by all organisms result in the formation of the 5'-deoxy-nucleoside byproducts, 5'-methylthioadenosine and 5'-deoxyadenosine. All E. coli possess a conserved nucleosidase that cleaves these 5'-deoxy-nucleosides into 5-deoxy-pentose sugars for adenine salvage. The DHAP shunt pathway is found in some extraintestinal pathogenic E. coli, but its function in E. coli possessing it has remained unknown. This study reveals that the DHAP shunt enables the utilization of 5'-deoxy-nucleosides and 5-deoxy-pentose sugars as growth substrates in E. coli strains with the pathway during aerobic respiration and anaerobic respiration with TMAO, but not fermentative growth. This provides an insight into the diversity of sugar compounds accessible by E. coli with the DHAP shunt and suggests that the DHAP shunt is primarily relevant in oxic or TMAO-rich extraintestinal environments.
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Affiliation(s)
| | - Joshua T. Groves
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - John A. Wildenthal
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - F. Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Justin A. North
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
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3
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Yang H, He Y, Zhou S, Deng Y. Dynamic regulation and cofactor engineering of escherichia coli to enhance production of glycolate from corn stover hydrolysate. BIORESOURCE TECHNOLOGY 2024; 398:130531. [PMID: 38447620 DOI: 10.1016/j.biortech.2024.130531] [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: 12/27/2023] [Revised: 02/24/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
Glycolic acid is widely employed in chemical cleaning, the production of polyglycolic acid-lactic acid, and polyglycolic acid. Currently, the bottleneck of glycolate biosynthesis lies on the imbalance of metabolic flux and the deficiency of NADPH. In this study, a dynamic regulation system was developed and optimized to enhance the metabolic flux from glucose to glycolate. Additionally, the knockout of transhydrogenase (sthA), along with the overexpression of pyridine nucleotide transhydrogenase (pntAB) and the implementation of the Entner-Doudoroff pathway, were performed to further increase the production of the NADPH, thereby increasing the titer of glycolate to 5.6 g/L. To produce glycolate from corn stover hydrolysate, carbon catabolite repression was alleviated and glucose utilization was accelerated. The final strain, E. coli Mgly10-245, is inducer-free, achieving a glycolate titer of 46.1 g/L using corn stover hydrolysate (77.1 % of theoretical yield). These findings will contribute to the advancement of industrial glycolate production.
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Affiliation(s)
- Haining Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yucai He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, China, 430062
| | - Shenghu Zhou
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Yu Deng
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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4
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Zheng H, Wang C, Yu X, Zheng W, An Y, Zhang J, Zhang Y, Wang G, Qi M, Lin H, Wang F. The Role of Metabolomics and Microbiology in Urinary Tract Infection. Int J Mol Sci 2024; 25:3134. [PMID: 38542107 PMCID: PMC10969911 DOI: 10.3390/ijms25063134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 08/25/2024] Open
Abstract
One of the common illnesses that affect women's physical and mental health is urinary tract infection (UTI). The disappointing results of empirical anti-infective treatment and the lengthy time required for urine bacterial culture are two issues. Antibiotic misuse is common, especially in females who experience recurrent UTI (rUTI). This leads to a higher prevalence of antibiotic resistance in the microorganisms that cause the infection. Antibiotic therapy will face major challenges in the future, prompting clinicians to update their practices. New testing techniques are making the potential association between the urogenital microbiota and UTIs increasingly apparent. Monitoring changes in female urinary tract (UT) microbiota, as well as metabolites, may be useful in exploring newer preventive treatments for UTIs. This review focuses on advances in urogenital microbiology and organismal metabolites relevant to the identification and handling of UTIs in an attempt to provide novel methods for the identification and management of infections of the UT. Particular attention is paid to the microbiota and metabolites in the patient's urine in relation to their role in supporting host health.
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Affiliation(s)
- Haoyu Zheng
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Chao Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Xiao Yu
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Wenxue Zheng
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Yiming An
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Jiaqi Zhang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Yuhan Zhang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Guoqiang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Mingran Qi
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Hongqiang Lin
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Fang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
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Law RC, Nurwono G, Park JO. A parallel glycolysis provides a selective advantage through rapid growth acceleration. Nat Chem Biol 2024; 20:314-322. [PMID: 37537378 PMCID: PMC10987256 DOI: 10.1038/s41589-023-01395-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
Glycolysis is a universal metabolic process that breaks down glucose to produce adenosine triphosphate (ATP) and biomass precursors. The Entner-Doudoroff (ED) pathway is a glycolytic pathway that parallels textbook glycolysis but yields half as much ATP. Accordingly, in organisms that possess both glycolytic pathways (for example, Escherichia coli), its raison d'être remains a mystery. In this study, we found that the ED pathway provides a selective advantage during growth acceleration. Upon carbon and nitrogen upshifts, E. coli accelerates growth faster with than without the ED pathway. Concurrent isotope tracing reveals that the ED pathway flux increases faster than that of textbook glycolysis. We attribute the fast response time of the ED pathway to its strong thermodynamic driving force and streamlining of glucose import. Intermittent nutrient supply manifests the evolutionary advantage of the parallel glycolysis; thus, the dynamic nature of an ostensibly redundant pathway's role in promoting rapid adaptation constitutes a metabolic design principle.
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Affiliation(s)
- Richard C Law
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Glenn Nurwono
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Junyoung O Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
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Miki S, Fukamachi H, Itsumi M, Fujiwara N, Takaki T, Kurosawa M, Morisaki H, Suzuki N, Kuwata H. The Klebsiella mannose phosphotransferase system promotes proliferation and the production of extracellular polymeric substances from mannose, facilitating adaptation to the host environment. J Oral Biosci 2024; 66:119-125. [PMID: 38246421 DOI: 10.1016/j.job.2024.01.003] [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: 12/01/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
OBJECTIVES Klebsiella spp., an opportunistic infectious organism, is commensal in the nasal and oral cavities of humans. Recently, it has been reported that oral Klebsiella spp. ectopically colonize the intestinal tract and induce the accumulation of intestinal Th1 cells. For oral bacteria to colonize the intestinal tract, they need to compete for nutrients with indigenous intestinal bacteria. Therefore, we focused on mannose, a mucus-derived sugar, and the mannose phosphotransferase system (PTS) (ManXYZ), a mechanism for mannose uptake, in terms of their effects on intestinal colonization and immune responses to Klebsiella spp. METHODS We generated a Klebsiella manXYZ-deficient strain and investigated whether the utilization of intestinal mucus-derived sugars is associated with the growth. Furthermore, we examine the virulence of this organism in the mouse intestinal tract, especially the ability to colonize the host using competition assay. RESULTS We found that Klebsiella ManXYZ is a PTS that specifically takes up mannose and glucosamine. Through ManXYZ, mannose was used for bacterial growth and the upregulated production of extracellular polymeric substances. In vivo competition assays showed that mannose metabolism promoted intestinal colonization. However, ManXYZ was not involved in Th1 and Th17 induction in the intestinal tract. CONCLUSION The fundamental roles of ManXYZ were to ensure that mannose, which is present in the host, is made available for bacterial growth, to promote the production of extracellular polymeric substances, thus facilitating bacterial adaptation to the host environment.
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Affiliation(s)
- Suguru Miki
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan; Department of Conservative Dentistry, Division of Endodontology, Showa University Graduate School of Dentistry, 2-1-1 Kitasenzoku, Ohta-ku, Tokyo, 145-8515, Japan
| | - Haruka Fukamachi
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan.
| | - Momoe Itsumi
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Nagatoshi Fujiwara
- Department of Food and Nutrition, Tezukayama University, Tezukayama 7-1-1, Nara City, Nara, 631-8585, Japan
| | - Takashi Takaki
- Center for Electron Microscopy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Mie Kurosawa
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Hirobumi Morisaki
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Noriyuki Suzuki
- Department of Conservative Dentistry, Division of Endodontology, Showa University Graduate School of Dentistry, 2-1-1 Kitasenzoku, Ohta-ku, Tokyo, 145-8515, Japan
| | - Hirotaka Kuwata
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
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Doranga S, Krogfelt KA, Cohen PS, Conway T. Nutrition of Escherichia coli within the intestinal microbiome. EcoSal Plus 2024:eesp00062023. [PMID: 38417452 DOI: 10.1128/ecosalplus.esp-0006-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/03/2023] [Indexed: 03/01/2024]
Abstract
In this chapter, we update our 2004 review of "The Life of Commensal Escherichia coli in the Mammalian Intestine" (https://doi.org/10.1128/ecosalplus.8.3.1.2), with a change of title that reflects the current focus on "Nutrition of E. coli within the Intestinal Microbiome." The earlier part of the previous two decades saw incremental improvements in understanding the carbon and energy sources that E. coli and Salmonella use to support intestinal colonization. Along with these investigations of electron donors came a better understanding of the electron acceptors that support the respiration of these facultative anaerobes in the gastrointestinal tract. Hundreds of recent papers add to what was known about the nutrition of commensal and pathogenic enteric bacteria. The fact that each biotype or pathotype grows on a different subset of the available nutrients suggested a mechanism for succession of commensal colonizers and invasion by enteric pathogens. Competition for nutrients in the intestine has also come to be recognized as one basis for colonization resistance, in which colonized strain(s) prevent colonization by a challenger. In the past decade, detailed investigations of fiber- and mucin-degrading anaerobes added greatly to our understanding of how complex polysaccharides support the hundreds of intestinal microbiome species. It is now clear that facultative anaerobes, which usually cannot degrade complex polysaccharides, live in symbiosis with the anaerobic degraders. This concept led to the "restaurant hypothesis," which emphasizes that facultative bacteria, such as E. coli, colonize the intestine as members of mixed biofilms and obtain the sugars they need for growth locally through cross-feeding from polysaccharide-degrading anaerobes. Each restaurant represents an intestinal niche. Competition for those niches determines whether or not invaders are able to overcome colonization resistance and become established. Topics centered on the nutritional basis of intestinal colonization and gastrointestinal health are explored here in detail.
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Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Karen A Krogfelt
- Department of Science and Environment, Pandemix Center Roskilde University, Roskilde, Denmark
| | - Paul S Cohen
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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Cotton S, Clayton CA, Tropini C. Microbial endocrinology: the mechanisms by which the microbiota influences host sex steroids. Trends Microbiol 2023; 31:1131-1142. [PMID: 37100633 DOI: 10.1016/j.tim.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 04/28/2023]
Abstract
Recent progress in microbial endocrinology has propelled this field from initially providing correlational links to defining the mechanisms by which microbes influence systemic sex hormones. Importantly, the interaction between the gut-resident bacteria and host-secreted hormones has been shown to be critical for host development as well as hormone-mediated disease progression. This review investigates how microbes affect active sex hormone levels, with a focus on gut-associated bacteria hormonal modifications and the resulting host physiological status. Specifically, we focus on the ability of the microbiota to reactivate estrogens and deactivate androgens and thereby influence systemic levels of host hormones in a clinically significant manner.
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Affiliation(s)
- Sophie Cotton
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Charlotte A Clayton
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Carolina Tropini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Canada.
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Honda K, Furuichi M, Kawaguchi T, Pust MM, Yasuma-Mitobe K, Plichta D, Hasegawa N, Ohya T, Bhattarai S, Sasajima S, Yoshimasa A, Tuganbaev T, Yaginuma M, Ueda M, Okahashi N, Amafuji K, Kiridooshi Y, Sugita K, Stražar M, Skelly A, Suda W, Hattori M, Nakamoto N, Caballero S, Norman J, Olle B, Tanoue T, Arita M, Bucci V, Atarashi K, Xavier R. Rationally-defined microbial consortia suppress multidrug-resistant proinflammatory Enterobacteriaceae via ecological control. RESEARCH SQUARE 2023:rs.3.rs-3462622. [PMID: 37961431 PMCID: PMC10635318 DOI: 10.21203/rs.3.rs-3462622/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Persistent colonization and outgrowth of pathogenic organisms in the intestine may occur due to long-term antibiotic usage or inflammatory conditions, which perpetuate dysregulated immunity and tissue damage1,2. Gram-negative Enterobacteriaceae gut pathobionts are particularly recalcitrant to conventional antibiotic treatment3,4, though an emerging body of evidence suggests that manipulation of the commensal microbiota may be a practical alternative therapeutic strategy5-7. In this study, we rationally isolated and down-selected commensal bacterial consortia from healthy human stool samples capable of strongly and specifically suppressing intestinal Enterobacteriaceae. One of the elaborated consortia, consisting of 18 commensal strains, effectively controlled ecological niches by regulating gluconate availability, thereby reestablishing colonization resistance and alleviating antibiotic-resistant Klebsiella-driven intestinal inflammation in mice. Harnessing these microbial activities in the form of live bacterial therapeutics may represent a promising solution to combat the growing threat of proinflammatory, antimicrobial-resistant bacterial infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Aoto Yoshimasa
- JSR-Keio University Medical and Chemical Innovation Center
| | | | | | | | | | | | | | | | | | | | - Wataru Suda
- RIKEN Center for Integrative Medical Sciences
| | | | | | - Silvia Caballero
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center
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Nakano H, Sakao K, Wada K, Hou DX. Ameliorative Effects of Anthocyanin Metabolites on Western Diet-Induced NAFLD by Modulating Co-Occurrence Networks of Gut Microbiome. Microorganisms 2023; 11:2408. [PMID: 37894066 PMCID: PMC10609007 DOI: 10.3390/microorganisms11102408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Anthocyanins (Acn) have been reported to have preventive effects on Western diet (WD)-induced non-alcoholic fatty liver disease (NAFLD). However, the amount of Acn that reached the bloodstream were less than 1%, suggesting that anthocyanin metabolites (Acn-M) in the gut may contribute to their in vivo effects. This study is focused on a gut microbiota investigation to elucidate the effect of two major Acn-M, protocatechuic acid (PC) and phloroglucinol carboxaldehyde (PG), on NAFLD prevention. C57BL/6N male mice were divided into five groups and fed with a normal diet (ND), WD, WD + 0.5% PC, WD + 0.5% PG and WD + a mixture of 0.25% PC + 0.25% PG (CG) for 12 weeks. The results revealed that WD-fed mice showed a significant increase in final body weight, epididymis fat weight, liver weight and fat accumulation rate, serum total cholesterol, alanine aminotransferase, monocyte chemoattractant protein 1, and 2-thiobarbituric acid reactive substances. At the same time, these indices were significantly decreased by Acn-M in the order of PG, CG > PC. In particular, PG significantly decreased serum glucose and insulin resistance. Gut microbiome analysis revealed that PG significantly increased the relative abundance of Parabacteroides, Prevotella, Prevotella/Bacteroides ratio, and upregulated glucose degradation pathway. Interestingly, the co-occurrence networks of Lachnospiraceae and Desulfovibrionaceae in the PC and PG groups were similar to the ND group and different to WD group. These data suggest that PC and PG were able to recover the gut microbiome networks and functions from dysbiosis caused by WD. Therefore, PG might act as a master metabolite for anthocyanins and prevent WD-induced NAFLD and gut dysbiosis.
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Affiliation(s)
- Hironobu Nakano
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; (H.N.); (K.S.); (K.W.)
| | - Kozue Sakao
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; (H.N.); (K.S.); (K.W.)
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Koji Wada
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; (H.N.); (K.S.); (K.W.)
- Department of Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara 903-0213, Japan
| | - De-Xing Hou
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan; (H.N.); (K.S.); (K.W.)
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
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11
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Pokorzynski ND, Groisman EA. How Bacterial Pathogens Coordinate Appetite with Virulence. Microbiol Mol Biol Rev 2023; 87:e0019822. [PMID: 37358444 PMCID: PMC10521370 DOI: 10.1128/mmbr.00198-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
Cells adjust growth and metabolism to nutrient availability. Having access to a variety of carbon sources during infection of their animal hosts, facultative intracellular pathogens must efficiently prioritize carbon utilization. Here, we discuss how carbon source controls bacterial virulence, with an emphasis on Salmonella enterica serovar Typhimurium, which causes gastroenteritis in immunocompetent humans and a typhoid-like disease in mice, and propose that virulence factors can regulate carbon source prioritization by modifying cellular physiology. On the one hand, bacterial regulators of carbon metabolism control virulence programs, indicating that pathogenic traits appear in response to carbon source availability. On the other hand, signals controlling virulence regulators may impact carbon source utilization, suggesting that stimuli that bacterial pathogens experience within the host can directly impinge on carbon source prioritization. In addition, pathogen-triggered intestinal inflammation can disrupt the gut microbiota and thus the availability of carbon sources. By coordinating virulence factors with carbon utilization determinants, pathogens adopt metabolic pathways that may not be the most energy efficient because such pathways promote resistance to antimicrobial agents and also because host-imposed deprivation of specific nutrients may hinder the operation of certain pathways. We propose that metabolic prioritization by bacteria underlies the pathogenic outcome of an infection.
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Affiliation(s)
- Nick D. Pokorzynski
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eduardo A. Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
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12
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Strategies to Enhance the Biosynthesis of Monounsaturated Fatty Acids in Escherichia coli. BIOTECHNOL BIOPROC E 2023. [DOI: 10.1007/s12257-022-0295-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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13
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Galhardo JP, Piffer AP, Fiamenghi MB, Borelli G, da Silva DRM, Vasconcelos AA, Carazzolle MF, Pereira GAG, José J. Wide distribution of D-xylose dehydrogenase in yeasts reveals a new element in the D-xylose metabolism for bioethanol production. FEMS Yeast Res 2023; 23:foad003. [PMID: 36731871 DOI: 10.1093/femsyr/foad003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/03/2023] [Accepted: 02/01/2023] [Indexed: 02/04/2023] Open
Abstract
D-xylose utilization by yeasts is an essential feature for improving second-generation ethanol production. However, industrial yeast strains are incapable of consuming D-xylose. Previous analyzes of D-xylose-consuming or fermenting yeast species reveal that the genomic features associated with this phenotype are complex and still not fully understood. Here we present a previously neglected yeast enzyme related to D-xylose metabolism, D-xylose dehydrogenase (XylDH), which is found in at least 105 yeast genomes. By analyzing the XylDH gene family, we brought evidence of gene evolution marked by purifying selection on codons and positive selection evidence in D-xylose-consuming and fermenting species, suggesting the importance of XylDH for D-xylose-related phenotypes in yeasts. Furthermore, although we found no putative metabolic pathway for XylDH in yeast genomes, namely the absence of three bacterial known pathways for this enzyme, we also provide its expression profile on D-xylose media following D-xylose reductase for two yeasts with publicly available transcriptomes. Based on these results, we suggest that XylDH plays an important role in D-xylose usage by yeasts, likely being involved in a cofactor regeneration system by reducing cofactor imbalance in the D-xylose reductase pathway.
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Affiliation(s)
- Juliana P Galhardo
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - André P Piffer
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Mateus B Fiamenghi
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Guilherme Borelli
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Duguay R M da Silva
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Adrielle A Vasconcelos
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Marcelo F Carazzolle
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Gonçalo A G Pereira
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Juliana José
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
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14
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Tutukina MN, Dakhnovets AI, Kaznadzey AD, Gelfand MS, Ozoline ON. Sense and antisense RNA products of the uxuR gene can affect motility and chemotaxis acting independent of the UxuR protein. Front Mol Biosci 2023; 10:1121376. [PMID: 36936992 PMCID: PMC10016265 DOI: 10.3389/fmolb.2023.1121376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Small non-coding and antisense RNAs are widespread in all kingdoms of life, however, the diversity of their functions in bacteria is largely unknown. Here, we study RNAs synthesised from divergent promoters located in the 3'-end of the uxuR gene, encoding transcription factor regulating hexuronate metabolism in Escherichia coli. These overlapping promoters were predicted in silico with rather high scores, effectively bound RNA polymerase in vitro and in vivo and were capable of initiating transcription in sense and antisense directions. The genome-wide correlation between in silico promoter scores and RNA polymerase binding in vitro and in vivo was higher for promoters located on the antisense strands of the genes, however, sense promoters within the uxuR gene were more active. Both regulatory RNAs synthesised from the divergent promoters inhibited expression of genes associated with the E. coli motility and chemotaxis independent of a carbon source on which bacteria had been grown. Direct effects of these RNAs were confirmed for the fliA gene encoding σ28 subunit of RNA polymerase. In addition to intracellular sRNAs, promoters located within the uxuR gene could initiate synthesis of transcripts found in the fraction of RNAs secreted in the extracellular medium. Their profile was also carbon-independent suggesting that intragenic uxuR transcripts have a specific regulatory role not directly related to the function of the protein in which gene they are encoded.
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Affiliation(s)
- Maria N. Tutukina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, FRC PRCBR, Pushchino, Russia
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
- *Correspondence: Maria N. Tutukina, , Olga N. Ozoline,
| | - Artemiy I. Dakhnovets
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Biotechnology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Anna D. Kaznadzey
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Mikhail S. Gelfand
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Olga N. Ozoline
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, FRC PRCBR, Pushchino, Russia
- *Correspondence: Maria N. Tutukina, , Olga N. Ozoline,
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15
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van ‘t Hof M, Mohite OS, Monk JM, Weber T, Palsson BO, Sommer MOA. High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. BMC Bioinformatics 2022; 23:566. [PMID: 36585633 PMCID: PMC9801561 DOI: 10.1186/s12859-022-05108-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Escherichia coli Nissle 1917 (EcN) is a probiotic bacterium used to treat various gastrointestinal diseases. EcN is increasingly being used as a chassis for the engineering of advanced microbiome therapeutics. To aid in future engineering efforts, our aim was to construct an updated metabolic model of EcN with extended secondary metabolite representation. RESULTS An updated high-quality genome-scale metabolic model of EcN, iHM1533, was developed based on comparison with 55 E. coli/Shigella reference GEMs and manual curation, including expanded secondary metabolite pathways (enterobactin, salmochelins, aerobactin, yersiniabactin, and colibactin). The model was validated and improved using phenotype microarray data, resulting in an 82.3% accuracy in predicting growth phenotypes on various nutrition sources. Flux variability analysis with previously published 13C fluxomics data validated prediction of the internal central carbon fluxes. A standardised test suite called Memote assessed the quality of iHM1533 to have an overall score of 89%. The model was applied by using constraint-based flux analysis to predict targets for optimisation of secondary metabolite production. Modelling predicted design targets from across amino acid metabolism, carbon metabolism, and other subsystems that are common or unique for influencing the production of various secondary metabolites. CONCLUSION iHM1533 represents a well-annotated metabolic model of EcN with extended secondary metabolite representation. Phenotype characterisation and the iHM1533 model provide a better understanding of the metabolic capabilities of EcN and will help future metabolic engineering efforts.
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Affiliation(s)
- Max van ‘t Hof
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Omkar S. Mohite
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jonathan M. Monk
- grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Tilmann Weber
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Bernhard O. Palsson
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark ,grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Morten O. A. Sommer
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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16
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Plaza-Díaz J, Manzano M, Ruiz-Ojeda FJ, Giron MD, Salto R, López-Pedrosa JM, Santos-Fandila A, Garcia-Corcoles MT, Rueda R, Gil Á. Intake of slow-digesting carbohydrates is related to changes in the microbiome and its functional pathways in growing rats with obesity induced by diet. Front Nutr 2022; 9:992682. [PMID: 36532542 PMCID: PMC9748084 DOI: 10.3389/fnut.2022.992682] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/02/2022] [Indexed: 08/17/2023] Open
Abstract
INTRODUCTION The main cause of insulin resistance in childhood is obesity, which contributes to future comorbidities as in adults. Although high-calorie diets and lack of exercise contribute to metabolic disease development, food quality rather than the quantity of macronutrients is more important than food density. The purpose of the present study was to examine the effects of changing the quality of carbohydrates from rapidly to slowly digestible carbohydrates on the composition of the gut microbiota and the profiles of the functional pathways in growing rats with obesity due to a high-fat diet (HFD). METHODS During the course of 4 weeks, rats growing on an HFD-containing carbohydrates with different digestive rates were fed either HFD-containing carbohydrates with a rapid digestion rate (OBE group) or HFD-containing carbohydrates with a slow digestion rate (OBE-ISR group). A non-obese group (NOB) was included as a reference, and rats were fed on a rodent standard diet (AIN93G). An analysis of gut microbiota was conducted using 16S rRNA-based metagenomics; a linear mixed-effects model (LMM) was used to determine changes in abundance between baseline and 4 weeks of treatment, and functional pathways were identified. Gut microbiota composition at bacterial diversity and relative abundance, at phylum and genus levels, and functional profiles were analyzed by integrating the Integrated Microbial Genomes (IMG) database. RESULTS The groups showed comparable gut microbiota at baseline. At the end of the treatment, animals from the ISR group exhibited differences at the phylum levels by decreasing the diversity of Fisher's index and Firmicutes (newly named as Bacillota), and increasing the Pielou's evenness and Bacteroidetes (newly named as Bacteroidota); at the genus level by increasing Alistipes, Bifidobacterium, Bacteroides, Butyricimonas, Lachnoclostridium, Flavonifractor, Ruminiclostridium 5, and Faecalibaculum and decreasing Muribaculum, Blautia, and Ruminiclostridium 9. Remarkably, relative abundances of genera Tyzzerella and Angelakisella were higher in the OBE group compared to NOB and OBE-ISR groups. In addition, some microbiota carbohydrate metabolism pathways such as glycolysis, glucuronic acid degradation, pentose phosphate pathway, methanogenesis, and fatty acid biosynthesis exhibited increased activity in the OBE-ISR group after the treatment. Higher levels of acetate and propionate were found in the feces of the ISR group compared with the NOB and OBE groups. CONCLUSION The results of this study demonstrate that replacing rapidly digestible carbohydrates with slowly digestible carbohydrates within an HFD improve the composition of the gut microbiota. Consequently, metabolic disturbances associated with obesity may be prevented.
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Affiliation(s)
- Julio Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Instituto de Investigación Biosanitaria de Granada (ibs.Granada), Complejo Hospitalario Universitario de Granada, Granada, Spain
| | | | - Francisco Javier Ruiz-Ojeda
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.Granada), Complejo Hospitalario Universitario de Granada, Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix”, Biomedical Research Centre, University of Granada, Granada, Spain
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Center Munich, Munich, Germany
| | - Maria D. Giron
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
| | - Rafael Salto
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
| | | | | | | | | | - Ángel Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.Granada), Complejo Hospitalario Universitario de Granada, Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix”, Biomedical Research Centre, University of Granada, Granada, Spain
- CIBER Physiopathology of Obesity and Nutrition, Instituto de Salud Carlos III, Madrid, Spain
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17
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Kim YE, Cho KH, Bang I, Kim CH, Ryu YS, Kim Y, Choi EM, Nong LK, Kim D, Lee SK. Characterization of an Entner-Doudoroff pathway-activated Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:120. [PMID: 36352474 PMCID: PMC9648032 DOI: 10.1186/s13068-022-02219-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Escherichia coli have both the Embden-Meyerhof-Parnas pathway (EMPP) and Entner-Doudoroff pathway (EDP) for glucose breakdown, while the EDP primarily remains inactive for glucose metabolism. However, EDP is a more favorable route than EMPP for the production of certain products. RESULTS EDP was activated by deleting the pfkAB genes in conjunction with subsequent adaptive laboratory evolution (ALE). The evolved strains acquired mutations in transcriptional regulatory genes for glycolytic process (crp, galR, and gntR) and in glycolysis-related genes (gnd, ptsG, and talB). The genotypic, transcriptomic and phenotypic analyses of those mutations deepen our understanding of their beneficial effects on cellulosic biomass bio-conversion. On top of these scientific understandings, we further engineered the strain to produce higher level of lycopene and 3-hydroxypropionic acid. CONCLUSIONS These results indicate that the E. coli strain has innate capability to use EDP in lieu of EMPP for glucose metabolism, and this versatility can be harnessed to further engineer E. coli for specific biotechnological applications.
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Affiliation(s)
- Ye Eun Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Kyung Hyun Cho
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Ina Bang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Chang Hee Kim
- Department of Biomedical Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Young Shin Ryu
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yuchan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Eun Mi Choi
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Department of Biomedical Engineering, UNIST, Ulsan, 44919, Republic of Korea.
| | - Sung Kuk Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Department of Biomedical Engineering, UNIST, Ulsan, 44919, Republic of Korea.
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18
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Letertre MPM, Bhatt AP, Harvey M, Nicholson JK, Wilson ID, Redinbo MR, Swann JR. Characterizing the metabolic effects of the selective inhibition of gut microbial β-glucuronidases in mice. Sci Rep 2022; 12:17435. [PMID: 36261446 PMCID: PMC9581996 DOI: 10.1038/s41598-022-21518-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/28/2022] [Indexed: 01/13/2023] Open
Abstract
The hydrolysis of xenobiotic glucuronides by gut bacterial glucuronidases reactivates previously detoxified compounds resulting in severe gut toxicity for the host. Selective bacterial β-glucuronidase inhibitors can mitigate this toxicity but their impact on wider host metabolic processes has not been studied. To investigate this the inhibitor 4-(8-(piperazin-1-yl)-1,2,3,4-tetrahydro-[1,2,3]triazino[4',5':4,5]thieno[2,3-c]isoquinolin-5-yl)morpholine (UNC10201652, Inh 9) was administered to mice to selectively inhibit a narrow range of bacterial β-glucuronidases in the gut. The metabolomic profiles of the intestinal contents, biofluids, and several tissues involved in the enterohepatic circulation were measured and compared to control animals. No biochemical perturbations were observed in the plasma, liver or gall bladder. In contrast, the metabolite profiles of urine, colon contents, feces and gut wall were altered compared to the controls. Changes were largely restricted to compounds derived from gut microbial metabolism. This work establishes that inhibitors targeted towards bacterial β-glucuronidases modulate the functionality of the intestinal microbiota without adversely impacting the host metabolic system.
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Affiliation(s)
- Marine P M Letertre
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- CNRS, CEISAM, UMR 6230, Nantes Université, 44000, Nantes, France
| | - Aadra P Bhatt
- Department of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Michael Harvey
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jeremy K Nicholson
- The Australian National Phenome Centre, Health Futures Institute, Murdoch University, Perth, Australia
- Institute of Global Health Innovation, Faculty of Medicine, Imperial College London, London, UK
| | - Ian D Wilson
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Matthew R Redinbo
- Departments of Chemistry, Biocemistry, Microbiology and Genomics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jonathan R Swann
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.
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19
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Bessonova TA, Fando MS, Kostareva OS, Tutukina MN, Ozoline ON, Gelfand MS, Nikulin AD, Tishchenko SV. Differential Impact of Hexuronate Regulators ExuR and UxuR on the Escherichia coli Proteome. Int J Mol Sci 2022; 23:ijms23158379. [PMID: 35955512 PMCID: PMC9369180 DOI: 10.3390/ijms23158379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/19/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
ExuR and UxuR are paralogous proteins belonging to the GntR family of transcriptional regulators. Both are known to control hexuronic acid metabolism in a variety of Gammaproteobacteria but the relative impact of each of them is still unclear. Here, we apply 2D difference electrophoresis followed by mass-spectrometry to characterise the changes in the Escherichia coli proteome in response to a uxuR or exuR deletion. Our data clearly show that the effects are different: deletion of uxuR resulted in strongly enhanced expression of D-mannonate dehydratase UxuA and flagellar protein FliC, and in a reduced amount of outer membrane porin OmpF, while the absence of ExuR did not significantly alter the spectrum of detected proteins. Consequently, the physiological roles of proteins predicted as homologs seem to be far from identical. Effects of uxuR deletion were largely dependent on the cultivation conditions: during growth with glucose, UxuA and FliC were dramatically altered, while during growth with glucuronate, activation of both was not so prominent. During the growth with glucose, maximal activation was detected for FliC. This was further confirmed by expression analysis and physiological tests, thus suggesting the involvement of UxuR in the regulation of bacterial motility and biofilm formation.
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Affiliation(s)
- Tatiana A. Bessonova
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
| | - Maria S. Fando
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Olga S. Kostareva
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Maria N. Tutukina
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30 Build 1, Moscow 121205, Russia;
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per 19 Build 1, Moscow 127051, Russia
- Correspondence:
| | - Olga N. Ozoline
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Institutskaya, 3, Pushchino 142290, Russia; (T.A.B.); (O.N.O.)
| | - Mikhail S. Gelfand
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30 Build 1, Moscow 121205, Russia;
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per 19 Build 1, Moscow 127051, Russia
| | - Alexey D. Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
| | - Svetlana V. Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya, 4, Pushchino 142290, Russia; (M.S.F.); (O.S.K.); (A.D.N.); (S.V.T.)
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20
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Differential Genetic Strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for Root Colonization of Oryza sativa subsp.
japonica
and O. sativa subsp.
indica
, as Revealed by Transposon Mutagenesis Sequencing. Appl Environ Microbiol 2022; 88:e0064222. [DOI: 10.1128/aem.00642-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Burkholderiaceae
are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of
Paraburkholderia
have repeatedly been described to stimulate plant growth.
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21
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Iacometti C, Marx K, Hönick M, Biletskaia V, Schulz-Mirbach H, Dronsella B, Satanowski A, Delmas VA, Berger A, Dubois I, Bouzon M, Döring V, Noor E, Bar-Even A, Lindner SN. Activating Silent Glycolysis Bypasses in Escherichia coli. BIODESIGN RESEARCH 2022; 2022:9859643. [PMID: 37850128 PMCID: PMC10521649 DOI: 10.34133/2022/9859643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/08/2022] [Indexed: 10/19/2023] Open
Abstract
All living organisms share similar reactions within their central metabolism to provide precursors for all essential building blocks and reducing power. To identify whether alternative metabolic routes of glycolysis can operate in E. coli, we complementarily employed in silico design, rational engineering, and adaptive laboratory evolution. First, we used a genome-scale model and identified two potential pathways within the metabolic network of this organism replacing canonical Embden-Meyerhof-Parnas (EMP) glycolysis to convert phosphosugars into organic acids. One of these glycolytic routes proceeds via methylglyoxal and the other via serine biosynthesis and degradation. Then, we implemented both pathways in E. coli strains harboring defective EMP glycolysis. Surprisingly, the pathway via methylglyoxal seemed to immediately operate in a triosephosphate isomerase deletion strain cultivated on glycerol. By contrast, in a phosphoglycerate kinase deletion strain, the overexpression of methylglyoxal synthase was necessary to restore growth of the strain. Furthermore, we engineered the "serine shunt" which converts 3-phosphoglycerate via serine biosynthesis and degradation to pyruvate, bypassing an enolase deletion. Finally, to explore which of these alternatives would emerge by natural selection, we performed an adaptive laboratory evolution study using an enolase deletion strain. Our experiments suggest that the evolved mutants use the serine shunt. Our study reveals the flexible repurposing of metabolic pathways to create new metabolite links and rewire central metabolism.
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Affiliation(s)
- Camillo Iacometti
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Katharina Marx
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Maria Hönick
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Viktoria Biletskaia
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Helena Schulz-Mirbach
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Beau Dronsella
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ari Satanowski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Valérie A. Delmas
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Anne Berger
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Ivan Dubois
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Madeleine Bouzon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Volker Döring
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Steffen N. Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Department of Biochemistry, Charité Universitätsmedizin, Virchowweg 6, 10117 Berlin, Germany
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22
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Aguilar-Lopez M, Wetzel C, MacDonald A, Ho TTB, Donovan SM. Metagenomic profile of the fecal microbiome of preterm infants consuming mother's own milk with bovine milk-based fortifier or infant formula: a cross-sectional study. Am J Clin Nutr 2022; 116:435-445. [PMID: 35383822 PMCID: PMC9638768 DOI: 10.1093/ajcn/nqac081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/29/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Preterm (PT) infants harbor a different gut microbiome than full-term infants. Multiple factors affect gut microbial colonization of PT infants, including low gestational age, high rates of Cesarean section, exposure to antibiotics, and diet. Human milk, whether it's mother's own milk (MOM) or donor human milk, is the preferred feeding mode for PT infants but needs to be fortified to achieve adequate nutrient content. Infant formulas are introduced at later stages if human milk is insufficient or unavailable. How these dietary exposures affect the gut microbiome of PT infants is poorly understood. OBJECTIVES The goal of this study was to evaluate the metagenomic potential of the fecal microbiome of PT infants consuming MOM with bovine milk-based fortifier compared with PT formula alone. METHODS Forty-two stool samples, from 27 infants consuming MOM or formula (21 samples in each group) were included. Twelve infants had repeated sampling (2-3 samples). Shotgun genomic DNA sequencing was performed and analyzed using MetaPhlAn and HUMAnN2. Multivariate regression analysis, adjusting by the repeated sampling, was used to identify the features that differed between PT infants consuming MOM compared with formula. RESULTS The primary function of the fecal microbiome of PT infants was characterized by a high abundance of biosynthesis pathways. A set of core features was identified; these belonged to pathways for amino acid metabolism and vitamin K-2 biosynthesis. Five pathways significantly differed between the MOM and formula group. Pathways for fatty acid and carbohydrate degradation were significantly higher in the MOM group. Taxonomically, members of the phylum Actinobacteria and the genus Bifidobacterium were higher in PT infants exposed to MOM. CONCLUSIONS This study provides insight into the influence of feeding MOM compared with infant formula on the structure and function of the fecal microbiome of PT infants.
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Affiliation(s)
- Miriam Aguilar-Lopez
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | | | - Thao T B Ho
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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23
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Virdis B, Hoelzle R, Marchetti A, Boto ST, Rosenbaum MA, Blasco-Gómez R, Puig S, Freguia S, Villano M. Electro-fermentation: Sustainable bioproductions steered by electricity. Biotechnol Adv 2022; 59:107950. [PMID: 35364226 DOI: 10.1016/j.biotechadv.2022.107950] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 02/22/2022] [Accepted: 03/24/2022] [Indexed: 01/06/2023]
Abstract
The market of biobased products obtainable via fermentation processes is steadily increasing over the past few years, driven by the need to create a decarbonized economy. To date, industrial fermentation (IF) employs either pure or mixed microbial cultures (MMC) whereby the type of the microbial catalysts and the used feedstock affect metabolic pathways and, in turn, the type of product(s) generated. In many cases, especially when dealing with MMC, the economic viability of IF is hindered by factors such as the low attained product titer and selectivity, which ultimately challenge the downstream recovery and purification steps. In this context, electro-fermentation (EF) represents an innovative approach, based on the use of a polarized electrode interface to trigger changes in the rate, yield, titer or product distribution deriving from traditional fermentation processes. In principle, the electrode in EF can act as an electron acceptor (i.e., anodic electro-fermentation, AEF) or donor (i.e., cathodic electro-fermentation, CEF), or simply as a mean to control the oxidation-reduction potential of the fermentation broth. However, the molecular and biochemical basis underlying the EF process are still largely unknown. This review paper provides a comprehensive overview of recent literature studies including both AEF and CEF examples with either pure or mixed microbial cultures. A critical analysis of biochemical, microbiological, and engineering aspects which presently hamper the transition of the EF technology from the laboratory to the market is also presented.
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Affiliation(s)
- Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert Hoelzle
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Angela Marchetti
- Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Santiago T Boto
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), 07745 Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University (FSU), 07743 Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), 07745 Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University (FSU), 07743 Jena, Germany
| | - Ramiro Blasco-Gómez
- LEQUIA, Institute of the Environment, University of Girona, Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Sebastià Puig
- LEQUIA, Institute of the Environment, University of Girona, Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Stefano Freguia
- Department of Chemical Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Marianna Villano
- Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy.
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24
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Candeliere F, Raimondi S, Ranieri R, Musmeci E, Zambon A, Amaretti A, Rossi M. β-Glucuronidase Pattern Predicted From Gut Metagenomes Indicates Potentially Diversified Pharmacomicrobiomics. Front Microbiol 2022; 13:826994. [PMID: 35308380 PMCID: PMC8928169 DOI: 10.3389/fmicb.2022.826994] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/21/2022] [Indexed: 11/16/2022] Open
Abstract
β-glucuronidases (GUS) of intestinal bacteria remove glucuronic acid from glucoronides, reversing phase II metabolism of the liver and affecting the level of active deconjugated metabolites deriving from drugs or xenobiotics. Two hundred seventy-nine non-redundant GUS sequences are known in the gut microbiota, classified in seven structural categories (NL, L1, L2, mL1, mL2, mL1,2, and NC) with different biocatalytic properties. In the present study, the intestinal metagenome of 60 healthy subjects from five geographically different cohorts was assembled, binned, and mined to determine qualitative and quantitative differences in GUS profile, potentially affecting response to drugs and xenobiotics. Each metagenome harbored 4–70 different GUS, altogether accounting for 218. The amount of intestinal bacteria with at least one GUS gene was highly variable, from 0.7 to 82.2%, 25.7% on average. No significant difference among cohorts could be identified, except for the Ethiopia (ETH) cohort where GUS-encoding bacteria were significantly less abundant. The structural categories were differently distributed among the metagenomes, but without any statistical significance related to the cohorts. GUS profiles were generally dominated by the category NL, followed by mL1, L2, and L1. The GUS categories most involved in the hydrolysis of small molecules, including drugs, are L1 and mL1. Bacteria contributing to these categories belonged to Bacteroides ovatus, Bacteroides dorei, Bacteroides fragilis, Escherichia coli, Eubacterium eligens, Faecalibacterium prausnitzii, Parabacteroides merdae, and Ruminococcus gnavus. Bacteria harboring L1 GUS were generally scarcely abundant (<1.3%), except in three metagenomes, where they reached up to 24.3% for the contribution of E. coli and F. prausnitzii. Bacteria harboring mL1 GUS were significantly more abundant (mean = 4.6%), with Bacteroides representing a major contributor. Albeit mL1 enzymes are less active than L1 ones, Bacteroides likely plays a pivotal role in the deglucuronidation, due to its remarkable abundance in the microbiomes. The observed broad interindividual heterogeneity of GUS profiles, particularly of the L1 and mL1 categories, likely represent a major driver of pharmacomicrobiomics variability, affecting drug response and toxicity. Different geographical origins, genetic, nutritional, and lifestyle features of the hosts seemed not to be relevant in the definition of glucuronidase activity, albeit they influenced the richness of the GUS profile.
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Affiliation(s)
- Francesco Candeliere
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Raffaella Ranieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Eliana Musmeci
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alfonso Zambon
- Department of Chemistry and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Biogest-Siteia, University of Modena and Reggio Emilia, Modena, Italy
| | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Biogest-Siteia, University of Modena and Reggio Emilia, Modena, Italy
- *Correspondence: Maddalena Rossi,
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25
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Jensen RH, Rønn M, Thorsteinsson M, Olijhoek DW, Nielsen MO, Nørskov NP. Untargeted Metabolomics Combined with Solid Phase Fractionation for Systematic Characterization of Bioactive Compounds in Hemp with Methane Mitigation Potential. Metabolites 2022; 12:metabo12010077. [PMID: 35050199 PMCID: PMC8779194 DOI: 10.3390/metabo12010077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
This study systematically evaluates the presence of methane mitigating metabolites in two hemp (Cannabis sativa L.) varieties, Futura 75 and Finola. Hemp metabolites were extracted with methanol and fractionated using Solid Phase Extraction (SPE). Extracts, fractions, and the remaining pulp were screened for their methane mitigating potential using an in vitro model of rumen fermentation. The bioactive metabolites were identified with Liquid Chromatography-Mass Spectrometry (LC-MS). When incubated with a standard feed (maize silage), the extract of Futura 75 significantly reduced methane production compared to that of control (without added extract) and without negative effects on feed degradability and volatile fatty acid patterns. The compounds responsible for the methane mitigating effect were assigned to flavonoid glycosides. However, none of the fractions of Futura 75 or the pulp exhibited similar effect on methane emission. Butyric acid concentration in the fermentation inoculum was significantly increased, which could indicate why methane production was higher, when incubated with the fractions and the pulp. The extract of Finola did not show a similar significant effect, however, there was a numerical tendency towards lower methane production. The difference in methane mitigating properties between Cannabis sativa L. Futura 75 and Finola, could be related to the content of bioactive flavonoids.
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26
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Abdelhamid Y, Wang M, Parkhill SL, Brear P, Chee X, Rahman T, Welch M. Structure, Function and Regulation of a Second Pyruvate Kinase Isozyme in Pseudomonas aeruginosa. Front Microbiol 2021; 12:790742. [PMID: 34867929 PMCID: PMC8637920 DOI: 10.3389/fmicb.2021.790742] [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: 10/07/2021] [Accepted: 10/26/2021] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas aeruginosa (PA) depends on the Entner-Doudoroff pathway (EDP) for glycolysis. The main enzymatic regulator in the lower half of the EDP is pyruvate kinase. PA contains genes that encode two isoforms of pyruvate kinase, denoted PykAPA and PykFPA. In other well-characterized organisms containing two pyruvate kinase isoforms (such as Escherichia coli) each isozyme is differentially regulated. The structure, function and regulation of PykAPA has been previously characterized in detail, so in this work, we set out to assess the biochemical and structural properties of the PykFPA isozyme. We show that pykF PA expression is induced in the presence of the diureide, allantoin. In spite of their relatively low amino acid sequence identity, PykAPA and PykFPA display broadly comparable kinetic parameters, and are allosterically regulated by a very similar set of metabolites. However, the x-ray crystal structure of PykFPA revealed significant differences compared with PykAPA. Notably, although the main allosteric regulator binding-site of PykFPA was empty, the "ring loop" covering the site adopted a partially closed conformation. Site-directed mutation of the proline residues flanking the ring loop yielded apparent "locked on" and "locked off" allosteric activation phenotypes, depending on the residue mutated. Analysis of PykFPA inter-protomer interactions supports a model in which the conformational transition(s) accompanying allosteric activation involve re-orientation of the A and B domains of the enzyme and subsequent closure of the active site.
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Affiliation(s)
- Yassmin Abdelhamid
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Meng Wang
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Xavier Chee
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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27
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Tishchenko SV, Mikhailina AO, Lekontseva NV, Stolboushkina EA, Nikonova EY, Nikonov OS, Nikulin AD. Structural Investigations of RNA–Protein Complexes in Post-Ribosomal Era. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Structural studies of RNA–protein complexes are important for understanding many molecular mechanisms occurring in cells (e.g., regulation of protein synthesis and RNA-chaperone activity of proteins). Various objects investigated at the Institute of Protein Research of the Russian Academy of Sciences are considered. Based on the analysis of the structures of the complexes of the ribosomal protein L1 with specific regions on both mRNA and rRNA, the principles of regulation of the translation of the mRNA of its own operon are presented. The studies of the heterotrimeric translation initiation factor IF2 of archaea and eukaryotes are described, and the data on the interaction of glycyl-tRNA-synthetase with viral IRES are reported. The results of studying the interaction of RNA molecules with one of functionally important sites of the Hfq protein are presented, and the differences in the RNA-binding properties of the Hfq and archaeal Lsm proteins are revealed.
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28
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Adnan F, Jalil A, Ahmed T, Rahman A, Dawood N, Haider G, Siddiqui MF, Rostock L, Guenther S, Schaufler K. TRAP transporter TakP: a key player in the resistance against selenite-induced oxidative stress in Rhodobacter sphaeroides. Microbiol Res 2021; 252:126828. [PMID: 34543948 DOI: 10.1016/j.micres.2021.126828] [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: 06/25/2020] [Revised: 03/28/2021] [Accepted: 07/20/2021] [Indexed: 11/24/2022]
Abstract
Almost one-third of all proteins require metal ions as an essential component in key biological processes and approximately half of all enzymes are associated with one or more metal ions. The naturally occurring selenium is very toxic at higher levels, but few bacteria can reduce it into the less toxic insoluble elemental selenium. Selenium is required for the synthesis of selenocysteine, an essential residue involved in the active sites of various enzymes. The purple non-sulphur bacteria, Rhodobacter sphaeroidesis demonstrated for its selenite reduction capacity. The exact mechanism of selenite toxicity is unknown but it reacts with glutathione to form selenodiglutathione, producing the highly toxic compounds namely, H2O2and O2-. A R. sphaeroidesstrain with mutated takP gene, a member of the TRAP (tripartite ATP-independent periplasmic) family of transporter, was reported to be showing more resistance towards selenite in the growth medium but the reason for the resistance is unknown. TRAP transporters are the best-studied family of substrate-binding protein and in our previous study it was confirmed that the gene takP in R. sphaeroides is down-regulated by a small non-coding RNA SorY, providing more resistance to the bacterium against the oxidative stress. By comparative growth analysis and sensitivity assays in the presence of 2 mM selenite, it was observed that the SorY knockout strain is more sensitive to selenite while overexpression of the sRNA conferred more resistance to the bacterium like the takP mutant strain. TakP is involved in the import of malate into the cell, which under oxidative stress needs to be down-regulated to limit malate flux into the cell. Limited malate flux leads to metabolic rearrangements in the cell to avoid excessive generation of prooxidant NADH and facilitate constant generation of antioxidant NADPH. In the presence and absence of selenite, a drastic increase in the NADPH and decrease in the NADH levels are reported respectively. Accumulation of metallic selenium in the cytoplasm was detected via atomic absorption spectrophotometer and our analysis clearly demonstrated the presence of more selenium in the electron micrographs of the SorY knockout strain compared to the takP mutant grown under dark semi-aerobic growth conditions in the presence of selenite. Hence based on our analysis, it is confirmed that lack of TakP transporter led to reduced selenite influx into the cytoplasm, relieving cells with limited generation of ROS, eventually exhibiting more resistance against selenite-induced oxidative stress.
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Affiliation(s)
- Fazal Adnan
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Amna Jalil
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Tahir Ahmed
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Afra Rahman
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Nawal Dawood
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | - Ghulam Haider
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, Pakistan.
| | | | - Leon Rostock
- Institute of Pharmacy, Pharmaceutical Biology, University of Greifswald, Germany.
| | - Sebastian Guenther
- Institute of Pharmacy, Pharmaceutical Biology, University of Greifswald, Germany.
| | - Katharina Schaufler
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, Germany; Institute of infection medicine, Kiel University, Germany.
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29
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Jayashree S, Sivakumar R, Karthikeyan R, Gunasekaran P, Rajendhran J. Genome-wide identification of probiotic Escherichia coli Nissle 1917 (EcN) fitness genes during adhesion to the intestinal epithelial cells Caco-2. Gene 2021; 803:145890. [PMID: 34375634 DOI: 10.1016/j.gene.2021.145890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/22/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
Escherichia coli Nissle 1917 (EcN) is an efficient probiotic strain extensively used worldwide because of its several health benefits. Adhesion to the intestinal cells is one of the prerequisites for a probiotic strain. To identify the genes essential for the adhesion of EcN on the intestinal cells, we utilized a quantitative genetic footprinting approach called transposon insertion sequencing (INSeq). A transposon insertion mutant library of EcN comprising of ~17,000 mutants was used to screen the adherence to the intestinal epithelial cells, Caco-2. The transposon insertion sites were identified from the input and output population by employing next-generation sequencing using the Ion torrent platform. Based on the relative abundance of reads in the input and output pools, we identified 113 candidate genes that are essential for the fitness of EcN during the adhesion and colonization on the Caco-2 cells. Functional categorization revealed that these fitness genes are associated with carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis, post-translational modification, stress response, motility and adhesion, and signal transduction. To further validate the genes identified in our INSeq analysis, we constructed individual knock-out mutants in five genes (cyclic di-GMP phosphodiesterase (gmp), hda, uidC, leuO, and hypothetical protein-coding gene). We investigated their ability to adhere to Caco-2 cells. Evaluation of these mutants showed reduced adhesion on Caco-2 cells, confirming their role in adhesion. Understanding the functions of these genes may provide novel insights into molecular regulation during colonization of probiotic bacteria to the intestinal cells, and useful to develop designer probiotic strains.
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Affiliation(s)
| | - Ramamoorthy Sivakumar
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Raman Karthikeyan
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | | | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India.
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30
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Schäfer L, Meinert-Berning C, Kobus S, Höppner A, Smits SHJ, Steinbüchel A. Crystal structure of the sugar acid-binding protein CxaP from a TRAP transporter in Advenella mimigardefordensis strain DPN7 T. FEBS J 2021; 288:4905-4917. [PMID: 33630388 DOI: 10.1111/febs.15789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 12/01/2022]
Abstract
Recently, CxaP, a sugar acid substrate binding protein (SBP) from Advenella mimigardefordensis strain DPN7T , was identified as part of a novel sugar uptake strategy. In the present study, the protein was successfully crystallized. Although several SBP structures of tripartite ATP-independent periplasmic transporters have already been solved, this is the first structure of an SBP accepting multiple sugar acid ligands. Protein crystals were obtained with bound d-xylonic acid, d-fuconic acid d-galactonic and d-gluconic acid, respectively. The protein shows the typical structure of an SBP of a tripartite ATP-independent periplasmic transporter consisting of two domains linked by a hinge and spanned by a long α-helix. By analysis of the structure, the substrate binding site of the protein was identified. The carboxylic group of the sugar acids interacts with Arg175, whereas the coordination of the hydroxylic groups at positions C2 and C3 is most probably realized by Arg154 and Asn151. Furthermore, it was observed that 2-keto-3-deoxy-d-gluconic acid is bound in protein crystals that were crystallized without the addition of any ligand, indicating that this molecule is prebound to the protein and is displaced by the other ligands if they are available. DATABASE: Structural data of CxaP complexes are available in the worldwide Protein Data Bank (https://www.rcsb.org) under the accession codes 7BBR (2-keto-3-deoxy-d-gluconic acid), 7BCR (d-galactonic acid), 7BCN (d-xylonic acid), 7BCO (d-fuconic acid) and 7BCP (d-gluconic acid).
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Affiliation(s)
- Lukas Schäfer
- Institute of Molecular Microbiology and Biotechnology, Westfälische Wilhelms University Münster, Münster, Germany
| | - Christina Meinert-Berning
- Institute of Molecular Microbiology and Biotechnology, Westfälische Wilhelms University Münster, Münster, Germany
| | - Stefanie Kobus
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Astrid Höppner
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexander Steinbüchel
- Institute of Molecular Microbiology and Biotechnology, Westfälische Wilhelms University Münster, Münster, Germany.,Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
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31
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Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917. Int J Mol Sci 2021; 22:ijms22042122. [PMID: 33672760 PMCID: PMC7924626 DOI: 10.3390/ijms22042122] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 01/03/2023] Open
Abstract
Escherichia coli Nissle 1917 (EcN) is an intestinal probiotic that is effective for the treatment of intestinal disorders, such as inflammatory bowel disease and ulcerative colitis. EcN is a representative Gram-negative probiotic in biomedical research and is an intensively studied probiotic. However, to date, its genome-wide metabolic network model has not been developed. Here, we developed a comprehensive and highly curated EcN metabolic model, referred to as iDK1463, based on genome comparison and phenome analysis. The model was improved and validated by comparing the simulation results with experimental results from phenotype microarray tests. iDK1463 comprises 1463 genes, 1313 unique metabolites, and 2984 metabolic reactions. Phenome data of EcN were compared with those of Escherichia coli intestinal commensal K-12 MG1655. iDK1463 was simulated to identify the genetic determinants responsible for the observed phenotypic differences between EcN and K-12. Further, the model was simulated for gene essentiality analysis and utilization of nutrient sources under anaerobic growth conditions. These analyses provided insights into the metabolic mechanisms by which EcN colonizes and persists in the gut. iDK1463 will contribute to the system-level understanding of the functional capacity of gut microbes and their interactions with microbiota and human hosts, as well as the development of live microbial therapeutics.
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Mao Q, Liu J, Wiertzema JR, Chen D, Chen P, Baumler DJ, Ruan R, Chen C. Identification of Quinone Degradation as a Triggering Event for Intense Pulsed Light-Elicited Metabolic Changes in Escherichia coli by Metabolomic Fingerprinting. Metabolites 2021; 11:metabo11020102. [PMID: 33578995 PMCID: PMC7916761 DOI: 10.3390/metabo11020102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 11/26/2022] Open
Abstract
Intense pulsed light (IPL) is becoming a new technical platform for disinfecting food against pathogenic bacteria. Metabolic changes are deemed to occur in bacteria as either the causes or the consequences of IPL-elicited bactericidal and bacteriostatic effects. However, little is known about the influences of IPL on bacterial metabolome. In this study, the IPL treatment was applied to E. coli K-12 for 0–20 s, leading to time- and dose-dependent reductions in colony-forming units (CFU) and morphological changes. Both membrane lipids and cytoplasmic metabolites of the control and IPL-treated E. coli were examined by the liquid chromatography-mass spectrometry (LC-MS)-based metabolomic fingerprinting. The results from multivariate modeling and marker identification indicate that the metabolites in electron transport chain (ETC), redox response, glycolysis, amino acid, and nucleotide metabolism were selectively affected by the IPL treatments. The time courses and scales of these metabolic changes, together with the biochemical connections among them, revealed a cascade of events that might be initiated by the degradation of quinone electron carriers and then followed by oxidative stress, disruption of intermediary metabolism, nucleotide degradation, and morphological changes. Therefore, the degradations of membrane quinones, especially the rapid depletion of menaquinone-8 (MK-8), can be considered as a triggering event in the IPL-elicited metabolic changes in E. coli.
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Affiliation(s)
- Qingqing Mao
- Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Ave, Saint Paul, MN 55108, USA; (Q.M.); (J.L.); (J.R.W.); (D.C.); (D.J.B.)
| | - Juer Liu
- Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Ave, Saint Paul, MN 55108, USA; (Q.M.); (J.L.); (J.R.W.); (D.C.); (D.J.B.)
| | - Justin R. Wiertzema
- Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Ave, Saint Paul, MN 55108, USA; (Q.M.); (J.L.); (J.R.W.); (D.C.); (D.J.B.)
| | - Dongjie Chen
- Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Ave, Saint Paul, MN 55108, USA; (Q.M.); (J.L.); (J.R.W.); (D.C.); (D.J.B.)
| | - Paul Chen
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 1390 Eckles Ave., Saint Paul, MN 55108, USA; (P.C.); (R.R.)
| | - David J. Baumler
- Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Ave, Saint Paul, MN 55108, USA; (Q.M.); (J.L.); (J.R.W.); (D.C.); (D.J.B.)
| | - Roger Ruan
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 1390 Eckles Ave., Saint Paul, MN 55108, USA; (P.C.); (R.R.)
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Ave, Saint Paul, MN 55108, USA; (Q.M.); (J.L.); (J.R.W.); (D.C.); (D.J.B.)
- Correspondence: ; Tel.: +1-612-624-7704; Fax: +1-612-625-5272
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Wang H, Wang Y, Humphris S, Nie W, Zhang P, Wright F, Campbell E, Hu B, Fan J, Toth I. Pectobacterium atrosepticum KDPG aldolase, Eda, participates in the Entner-Doudoroff pathway and independently inhibits expression of virulence determinants. MOLECULAR PLANT PATHOLOGY 2021; 22:271-283. [PMID: 33301200 PMCID: PMC7814964 DOI: 10.1111/mpp.13025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 05/22/2023]
Abstract
Pectobacterium carotovorum has an incomplete Entner-Doudoroff (ED) pathway, including enzyme 2-keto-3-deoxy-6-phosphogluconate aldolase (Eda) but lacking phosphogluconate dehydratase (Edd), while P. atrosepticum (Pba) has a complete pathway. To understand the role of the ED pathway in Pectobacterium infection, mutants of these two key enzymes, Δeda and Δedd, were constructed in Pba SCRI1039. Δeda exhibited significant decreased virulence on potato tubers and colonization in planta and was greatly attenuated in pectinase activity and the ability to use pectin breakdown products, including polygalacturonic acid (PGA) and galacturonic acid. These reduced phenotypes were restored following complementation with an external vector expressing eda. Quantitative reverse transcription PCR analysis revealed that expression of the pectinase genes pelA, pelC, pehN, pelW, and pmeB in Δeda cultured in pyruvate, with or without PGA, was significantly reduced compared to the wild type, while genes for virulence regulators (kdgR, hexR, hexA, and rsmA) remained unchanged. However, Δedd showed similar phenotypes to the wild type. To our knowledge, this is the first demonstration that disruption of eda has a feedback effect on inhibiting pectin degradation and that Eda is involved in building the arsenal of pectinases needed during infection by Pectobacterium.
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Affiliation(s)
- Huan Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
- Cell and Molecular ScienceJames Hutton InstituteDundeeUK
- Institute of Agricultural Science of Taihu Lake DistrictSuzhouChina
| | - Yujie Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Sonia Humphris
- Cell and Molecular ScienceJames Hutton InstituteDundeeUK
| | - Weihua Nie
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Pengfei Zhang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Frank Wright
- Bioinformatics and StatisticsJames Hutton InstituteDundeeUK
| | - Emma Campbell
- Cell and Molecular ScienceJames Hutton InstituteDundeeUK
| | - Baishi Hu
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Jiaqin Fan
- Department of Plant PathologyNanjing Agricultural UniversityNanjingChina
| | - Ian Toth
- Cell and Molecular ScienceJames Hutton InstituteDundeeUK
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Lin Z, Sun Y, Liu Y, Tong S, Shang Z, Cai Y, Lin W. Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket. Front Microbiol 2020; 11:590330. [PMID: 33224125 PMCID: PMC7674646 DOI: 10.3389/fmicb.2020.590330] [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: 08/01/2020] [Accepted: 10/20/2020] [Indexed: 11/21/2022] Open
Abstract
The transcription repressor of D-galactonate metabolism, DgoR, from Escherichia coli belongs to the FadR family of the GntR superfamily. In the presence of D-galactonate, DgoR binds to two inverted repeats overlapping the dgo cis-acting promoter repressing the expression of genes involved in D-galactonate metabolism. To further understand the structural and molecular details of ligand and effector interactions between D-galactonate and this FadR family member, herein we solved the crystal structure of C-terminal domain of DgoR (DgoR_C), which revealed a unique divalent metal-containing substrate binding pocket. The metal ion is required for D-galactonate binding, as evidenced by the dramatically decreased affinity between D-galactonate and DgoR in the presence of EDTA, which can be reverted by the addition of Zn2+, Mg2+, and Ca2+. The key amino acid residues involved in the interactions between D-galactonate and DgoR were revealed by molecular docking studies and further validated with biochemical studies by site-directed mutagenesis. It was found that changes to alanine in residues R102, W181, T191, and R224 resulted in significantly decreased binding affinities for D-galactonate, as determined by EMSA and MST assays. These results suggest that the molecular modifications induced by a D-galactonate and a metal binding in the DgoR are required for DNA binding activity and consequently, transcriptional inhibition.
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Affiliation(s)
- Zhaozhu Lin
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yi Sun
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yu Liu
- Department of Chemistry, Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States
| | - Shujuan Tong
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhuo Shang
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanheng Cai
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, NY, United States
| | - Wei Lin
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
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35
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Arya G, Pal M, Sharma M, Singh B, Singh S, Agrawal V, Chaba R. Molecular insights into effector binding by DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism in Escherichia coli. Mol Microbiol 2020; 115:591-609. [PMID: 33068046 DOI: 10.1111/mmi.14625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 01/23/2023]
Abstract
Several GntR/FadR transcriptional regulators govern sugar acid metabolism in bacteria. Although effectors have been identified for a few sugar acid regulators, the mode of effector binding is unknown. Even in the overall FadR subfamily, there are limited details on effector-regulator interactions. Here, we identified the effector-binding cavity in Escherichia coli DgoR, a FadR subfamily transcriptional repressor of D-galactonate metabolism that employs D-galactonate as its effector. Using a genetic screen, we isolated several dgoR superrepressor alleles. Blind docking suggested eight amino acids corresponding to these alleles to form a part of the effector-binding cavity. In vivo and in vitro assays showed that these mutations compromise the inducibility of DgoR without affecting its oligomeric status or affinity for target DNA. Taking Bacillus subtilis GntR as a representative, we demonstrated that the effector-binding cavity is similar among FadR subfamily sugar acid regulators. Finally, a comparison of sugar acid regulators with other FadR members suggested conserved features of effector-regulator recognition within the FadR subfamily. Sugar acid metabolism is widely implicated in bacterial colonization and virulence. The present study sets the basis to investigate the influence of natural genetic variations in FadR subfamily regulators on their sensitivity to sugar acids and ultimately on host-bacterial interactions.
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Affiliation(s)
- Garima Arya
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Mohinder Pal
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, India
| | - Bhupinder Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Swati Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Vishal Agrawal
- Department of Biochemistry, Panjab University, Chandigarh, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
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36
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Abstract
The Embden–Meyerhof–Parnas (EMP) and Entner–Doudoroff (ED) pathways are considered the most abundant catabolic pathways found in microorganisms, and ED enzymes have been shown to also be widespread in cyanobacteria, algae and plants. In a large number of organisms, especially common strains used in molecular biology, these pathways account for the catabolism of glucose. The existence of pathways for other carbohydrates that are relevant to biomass utilization has been recognized as new strains have been characterized among thermophilic bacteria and Archaea that are able to transform simple polysaccharides from biomass to more complex and potentially valuable precursors for industrial microbiology. Many of the variants of the ED pathway have the key dehydratase enzyme involved in the oxidation of sugar derived from different families such as the enolase, IlvD/EDD and xylose-isomerase-like superfamilies. There are the variations in structure of proteins that have the same specificity and generally greater-than-expected substrate promiscuity. Typical biomass lignocellulose has an abundance of xylan, and four different pathways have been described, which include the Weimberg and Dahms pathways initially oxidizing xylose to xylono-gamma-lactone/xylonic acid, as well as the major xylose isomerase pathway. The recent realization that xylan constitutes a large proportion of biomass has generated interest in exploiting the compound for value-added precursors, but few chassis microorganisms can grow on xylose. Arabinose is part of lignocellulose biomass and can be metabolized with similar pathways to xylose, as well as an oxidative pathway. Like enzymes in many non-phosphorylative carbohydrate pathways, enzymes involved in L-arabinose pathways from bacteria and Archaea show metabolic and substrate promiscuity. A similar multiplicity of pathways was observed for other biomass-derived sugars such as L-rhamnose and L-fucose, but D-mannose appears to be distinct in that a non-phosphorylative version of the ED pathway has not been reported. Many bacteria and Archaea are able to grow on mannose but, as with other minor sugars, much of the information has been derived from whole cell studies with additional enzyme proteins being incorporated, and so far, only one synthetic pathway has been described. There appears to be a need for further discovery studies to clarify the general ability of many microorganisms to grow on the rarer sugars, as well as evaluation of the many gene copies displayed by marine bacteria.
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37
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Flamholz AI, Dugan E, Blikstad C, Gleizer S, Ben-Nissan R, Amram S, Antonovsky N, Ravishankar S, Noor E, Bar-Even A, Milo R, Savage DF. Functional reconstitution of a bacterial CO 2 concentrating mechanism in Escherichia coli. eLife 2020; 9:59882. [PMID: 33084575 PMCID: PMC7714395 DOI: 10.7554/elife.59882] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Many photosynthetic organisms employ a CO2 concentrating mechanism (CCM) to increase the rate of CO2 fixation via the Calvin cycle. CCMs catalyze ≈50% of global photosynthesis, yet it remains unclear which genes and proteins are required to produce this complex adaptation. We describe the construction of a functional CCM in a non-native host, achieved by expressing genes from an autotrophic bacterium in an Escherichia coli strain engineered to depend on rubisco carboxylation for growth. Expression of 20 CCM genes enabled E. coli to grow by fixing CO2 from ambient air into biomass, with growth in ambient air depending on the components of the CCM. Bacterial CCMs are therefore genetically compact and readily transplanted, rationalizing their presence in diverse bacteria. Reconstitution enabled genetic experiments refining our understanding of the CCM, thereby laying the groundwork for deeper study and engineering of the cell biology supporting CO2 assimilation in diverse organisms.
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Affiliation(s)
- Avi I Flamholz
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Eli Dugan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Shira Amram
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Sumedha Ravishankar
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant PhysiologyPotsdamGermany
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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38
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Burin R, Shah DH. Global transcriptional profiling of tyramine and d-glucuronic acid catabolism in Salmonella. Int J Med Microbiol 2020; 310:151452. [PMID: 33091748 DOI: 10.1016/j.ijmm.2020.151452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/13/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022] Open
Abstract
Salmonella has evolved various metabolic pathways to scavenge energy from the metabolic byproducts of the host gut microbiota, however, the precise metabolic byproducts and pathways utilized by Salmonella remain elusive. Previously we reported that Salmonella can proliferate by deriving energy from two metabolites that naturally occur in the host as gut microbial metabolic byproducts, namely, tyramine (TYR, an aromatic amine) and d-glucuronic acid (DGA, a hexuronic acid). Salmonella Pathogenicity Island 13 (SPI-13) plays a critical role in the ability of Salmonella to derive energy from TYR and DGA, however the catabolic pathways of these two micronutrients in Salmonella are poorly defined. The objective of this study was to identify the specific genetic components and construct the regulatory circuits for the TYR and DGA catabolic pathways in Salmonella. To accomplish this, we employed TYR and DGA-induced global transcriptional profiling and gene functional network analysis approaches. We report that TYR induced differential expression of 319 genes (172 up-regulated and 157 down-regulated) when Salmonella was grown in the presence of TYR as a sole energy source. These included the genes originally predicted to be involved in the classical TYR catabolic pathway. TYR also induced expression of majority of genes involved in the acetaldehyde degradation pathway and aided identification of a few new genes that are likely involved in alternative pathway for TYR catabolism. In contrast, DGA induced differential expression of 71 genes (58 up-regulated and 13 down-regulated) when Salmonella was grown in the presence of DGA as a sole energy source. These included the genes originally predicted to be involved in the classical pathway and a few new genes likely involved in the alternative pathway for DGA catabolism. Interestingly, DGA also induced expression of SPI-2 T3SS, suggesting that DGA may also influence nutritional virulence of Salmonella. In summary, this is the first report describing the global transcriptional profiling of TYR and DGA catabolic pathways of Salmonella. This study will contribute to the better understanding of the role of TYR and DGA in metabolic adaptation and virulence of Salmonella.
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Affiliation(s)
- Raquel Burin
- Department of Veterinary Microbiology and Pathology, United States
| | - Devendra H Shah
- Department of Veterinary Microbiology and Pathology, United States; Paul Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, 99164-7040, United States.
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39
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Golder T, Mukhopadhyay AK, Koley H, Nandy RK. Nonmetabolizable Arabinose Inhibits Vibrio cholerae Growth in M9 Medium with Gluconate as the Sole Carbon Source. Jpn J Infect Dis 2020; 73:343-348. [PMID: 32350213 DOI: 10.7883/yoken.jjid.2019.304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The serogroups O1 and O139 of the marine bacterium Vibrio cholerae are responsible for causing cholera in humans. The pentose sugar arabinose is nonmetabolizable by the pathogen and is present in environmental niches as well as in the human intestine. In this study, arabinose-mediated V. cholerae growth interference was assessed in M9 minimal medium containing gluconate as the sole carbon source in the light of Entner-Doudoroff (ED) pathway, an obligatory metabolic route for gluconate utilization. V. cholerae O1 and O139 strains failed to grow in the presence of ≥ 0.3% arabinose in M9 with 0.2% gluconate, but there was no growth inhibition in the presence of arabinose in M9 with 0.2% glucose. Transcriptional analysis of edd and eda, the genes constituting the ED pathway, showed ~100- and ~17-fold increases, respectively, in M9-gluconate. Minor increases of ~4- and ~2-fold for edd and eda, respectively, were noted in AKI medium supplemented with 0.5% arabinose. The observed arabinose-mediated growth inhibition can contribute toward deepening the understanding of altered phenotypes, if any, via complementation/expression studies in V. cholerae with pBAD vectors and arabinose as an inducer.
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Affiliation(s)
- Taniya Golder
- ICMR-National Institute of Cholera and Enteric Diseases (NICED), India
| | | | - Hemanta Koley
- ICMR-National Institute of Cholera and Enteric Diseases (NICED), India
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40
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Jen FEC, Scott AL, Tan A, Seib KL, Jennings MP. Random Switching of the ModA11 Type III DNA Methyltransferase of Neisseria meningitidis Regulates Entner-Doudoroff Aldolase Expression by a Methylation Change in the eda Promoter Region. J Mol Biol 2020; 432:5835-5842. [PMID: 32896529 DOI: 10.1016/j.jmb.2020.08.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 11/16/2022]
Abstract
Phase-variable DNA methyltransferases (Mods) mediate epigenetic regulation of gene expression. These phase-variable regulons, called phasevarions, have been shown to regulate virulence and immunoevasion in multiple bacterial pathogens. How genome methylation switching mediates gene regulation is unresolved. Neisseria meningitidis remains a major cause of sepsis and meningitis worldwide. Previously, we reported that phase variation (rapid on/off switching) of the meningococcal ModA11 methyltransferase regulates 285 genes. Here we show a bioinformatic analysis that reveals only 26 of the regulated genes have a methylation site located upstream of the gene with potential for direct effect of methylation on transcription. To investigate how methylation changes are "read" to alter gene expression, we used a lacZ gene fusion approach. We showed a 182-nucleotide region upstream of the eda gene (Entner-Doudoroff aldolase) is sufficient to impart methylation-dependent regulation of eda. Site-directed mutagenesis of the 5'-ACGTm6AGG-3' ModA11 site upstream of the eda gene showed that methylation of this site modulates eda expression. We show that eda is regulated by the PhoB homolog MisR, and that a MisR binding motif overlaps with the ModA11 methylation site. In a MisR mutant, regulation of eda is uncoupled from regulation by ModA11 phasevarion switching. The on/off switching of ModA11 leads to the presence or absence of a N6-methyladenine modification at thousands of sites in the genome. Most of these modifications have no impact on gene regulation. Moreover, the majority of the 285 gene regulon that is controlled by ModA11 phasevarion switching (259/285) are not directly controlled by methylation changes in the promoter region of the regulated genes. Our data are consistent with direct control via methylation of a subset of the regulon, like Eda, whose regulation will trigger secondary effects in expression of many genes.
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Affiliation(s)
- Freda E-C Jen
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Adeana L Scott
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Aimee Tan
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia.
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Kitichalermkiat A, Katsuki M, Sato J, Sonoda T, Masuda Y, Honjoh KI, Miyamoto T. Effect of epigallocatechin gallate on gene expression of Staphylococcus aureus. J Glob Antimicrob Resist 2020; 22:854-859. [DOI: 10.1016/j.jgar.2020.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/26/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
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42
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Chen F, Köppen K, Rydzewski K, Einenkel R, Morguet C, Vu DT, Eisenreich W, Heuner K. Myo-Inositol as a carbon substrate in Francisella and insights into the metabolism of Francisella sp. strain W12-1067. Int J Med Microbiol 2020; 310:151426. [PMID: 32444321 DOI: 10.1016/j.ijmm.2020.151426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 04/06/2020] [Accepted: 04/29/2020] [Indexed: 12/29/2022] Open
Abstract
Recently, a new environmental Francisella strain, Francisella sp. strain W12-1067, has been identified in Germany. This strain is negative for the Francisella pathogenicity island (FPI) but exhibits a putative alternative type VI secretion system. Some known virulence factors of Francisella are present, but the pathogenic capacity of this species is not known yet. In silico genome analysis reveals the presence of a gene cluster tentatively enabling myo-inositol (MI) utilization via a putative inositol oxygenase. Labelling experiments starting from 2H-inositol demonstrate that this gene cluster is indeed involved in the metabolism of MI. We further show that, under in vitro conditions, supply of MI increases growth rates of strain W12-1067 in the absence of glucose and that the metabolism of MI is strongly reduced in a W12-1067 mutant lacking the MI gene cluster. The positive growth effect of MI in the absence of glucose is restored in this mutant strain by introducing the complete MI gene cluster. F. novicida Fx1 is also positive for the MI metabolizing gene cluster and MI again increases growth in a glucose-free medium, in contrast to F. novicida strain U112, which is shown to be a natural mutant of the MI metabolizing gene cluster. Labelling experiments of Francisella sp. strain W12-1067 in medium T containing 13C-glucose, 13C-serine or 13C-glycerol as tracers suggest a bipartite metabolism where glucose is mainly metabolized through glycolysis, but not through the Entner-Doudoroff pathway or the pentose phosphate pathway. Carbon flux from 13C-glycerol and 13C-serine is less active, and label from these tracers is transferred mostly into amino acids, lactate and fatty acids. Together, the metabolism of Francisella sp. strain W12-1067 seems to be more related to the respective one in F. novicida rather than in F. tularensis subsp. holarctica.
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Affiliation(s)
- Fan Chen
- Department of Chemistry, Chair of Biochemistry, Technische Universität München, Garching, Germany
| | - Kristin Köppen
- Working Group: Cellular Interactions of Bacterial Pathogens, Centre for Biological Threats and Special Pathogens, ZBS 2, Robert Koch Institute, Berlin, Germany
| | - Kerstin Rydzewski
- Working Group: Cellular Interactions of Bacterial Pathogens, Centre for Biological Threats and Special Pathogens, ZBS 2, Robert Koch Institute, Berlin, Germany
| | - Rosa Einenkel
- Working Group: Cellular Interactions of Bacterial Pathogens, Centre for Biological Threats and Special Pathogens, ZBS 2, Robert Koch Institute, Berlin, Germany
| | - Clara Morguet
- Department of Chemistry, Chair of Biochemistry, Technische Universität München, Garching, Germany
| | - Duc Tung Vu
- Department of Chemistry, Chair of Biochemistry, Technische Universität München, Garching, Germany
| | - Wolfgang Eisenreich
- Department of Chemistry, Chair of Biochemistry, Technische Universität München, Garching, Germany.
| | - Klaus Heuner
- Working Group: Cellular Interactions of Bacterial Pathogens, Centre for Biological Threats and Special Pathogens, ZBS 2, Robert Koch Institute, Berlin, Germany.
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Himpsl SD, Shea AE, Zora J, Stocki JA, Foreman D, Alteri CJ, Mobley HLT. The oxidative fumarase FumC is a key contributor for E. coli fitness under iron-limitation and during UTI. PLoS Pathog 2020; 16:e1008382. [PMID: 32106241 PMCID: PMC7064253 DOI: 10.1371/journal.ppat.1008382] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/10/2020] [Accepted: 02/05/2020] [Indexed: 01/17/2023] Open
Abstract
The energy required for a bacterium to grow and colonize the host is generated by metabolic and respiratory functions of the cell. Proton motive force, produced by these processes, drives cellular mechanisms including redox balance, membrane potential, motility, acid resistance, and the import and export of substrates. Previously, disruption of succinate dehydrogenase (sdhB) and fumarate reductase (frdA) within the oxidative and reductive tricarboxylic acid (TCA) pathways in uropathogenic E. coli (UPEC) CFT073 indicated that the oxidative, but not the reductive TCA pathway, is required for fitness in the urinary tract. Those findings led to the hypothesis that fumA and fumC encoding fumarase enzymes of the oxidative TCA cycle would be required for UPEC colonization, while fumB of the reductive TCA pathway would be dispensable. However, only UPEC strains lacking fumC had a fitness defect during experimental urinary tract infection (UTI). To further characterize the role of respiration in UPEC during UTI, additional mutants disrupting both the oxidative and reductive TCA pathways were constructed. We found that knock-out of frdA in the sdhB mutant strain background ameliorated the fitness defect observed in the bladder and kidneys for the sdhB mutant strain and results in a fitness advantage in the bladder during experimental UTI. The fitness defect was restored in the sdhBfrdA double mutant by complementation with frdABCD. Taken together, we demonstrate that it is not the oxidative or reductive pathway that is important for UPEC fitness per se, but rather only the oxidative TCA enzyme FumC. This fumarase lacks an iron-sulfur cluster and is required for UPEC fitness during UTI, most likely acting as a counter measure against exogenous stressors, especially in the iron-limited bladder niche.
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Affiliation(s)
- Stephanie D. Himpsl
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Allyson E. Shea
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jonathan Zora
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jolie A. Stocki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Dannielle Foreman
- Department of Natural Sciences, University of Michigan Dearborn, Dearborn, Michigan, United States of America
| | - Christopher J. Alteri
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Natural Sciences, University of Michigan Dearborn, Dearborn, Michigan, United States of America
- * E-mail:
| | - Harry L. T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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44
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Valk LC, Luttik MAH, de Ram C, Pabst M, van den Broek M, van Loosdrecht MCM, Pronk JT. A Novel D-Galacturonate Fermentation Pathway in Lactobacillus suebicus Links Initial Reactions of the Galacturonate-Isomerase Route With the Phosphoketolase Pathway. Front Microbiol 2020; 10:3027. [PMID: 32010092 PMCID: PMC6978723 DOI: 10.3389/fmicb.2019.03027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/17/2019] [Indexed: 11/13/2022] Open
Abstract
D-galacturonate, a key constituent of pectin, is a ubiquitous monomer in plant biomass. Anaerobic, fermentative conversion of D-galacturonate is therefore relevant in natural environments as well as in microbial processes for microbial conversion of pectin-containing agricultural residues. In currently known microorganisms that anaerobically ferment D-galacturonate, its catabolism occurs via the galacturonate-isomerase pathway. Redox-cofactor balancing in this pathway strongly constrains the possible range of products generated from anaerobic D-galacturonate fermentation, resulting in acetate as the predominant organic fermentation product. To explore metabolic diversity of microbial D-galacturonate fermentation, anaerobic enrichment cultures were performed at pH 4. Anaerobic batch and chemostat cultures of a dominant Lactobacillus suebicus strain isolated from these enrichment cultures produced near-equimolar amounts of lactate and acetate from D-galacturonate. A combination of whole-genome sequence analysis, quantitative proteomics, enzyme activity assays in cell extracts, and in vitro product identification demonstrated that D-galacturonate metabolism in L. suebicus occurs via a novel pathway. In this pathway, mannonate generated by the initial reactions of the canonical isomerase pathway is converted to 6-phosphogluconate by two novel biochemical reactions, catalyzed by a mannonate kinase and a 6-phosphomannonate 2-epimerase. Further catabolism of 6-phosphogluconate then proceeds via known reactions of the phosphoketolase pathway. In contrast to the classical isomerase pathway for D-galacturonate catabolism, the novel pathway enables redox-cofactor-neutral conversion of D-galacturonate to ribulose-5-phosphate. While further research is required to identify the structural genes encoding the key enzymes for the novel pathway, its redox-cofactor coupling is highly interesting for metabolic engineering of microbial cell factories for conversion of pectin-containing feedstocks into added-value fermentation products such as ethanol or lactate. This study illustrates the potential of microbial enrichment cultivation to identify novel pathways for the conversion of environmentally and industrially relevant compounds.
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Affiliation(s)
| | | | | | | | | | | | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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45
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Jimenez AG, Ellermann M, Abbott W, Sperandio V. Diet-derived galacturonic acid regulates virulence and intestinal colonization in enterohaemorrhagic Escherichia coli and Citrobacter rodentium. Nat Microbiol 2019; 5:368-378. [PMID: 31873206 PMCID: PMC6992478 DOI: 10.1038/s41564-019-0641-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 11/11/2019] [Indexed: 12/21/2022]
Abstract
Enteric pathogens sense the complex chemistry within the gastrointestinal (GI) tract to efficiently compete with the resident microbiota and establish a colonization niche. Here we show that enterohemorrhagic E. coli (EHEC), and its surrogate murine infection model Citrobacter rodentium, sense galacturonic-acid to initiate a multi-layered program towards successful mammalian infection. Galacturonic-acid utilization as a carbon source aids the initial pathogen expansion. The main source of galacturonic-acid is dietary pectin, which is broken into galacturonic-acid by the prominent member of the microbiota, Bacteroides thetaiotamicron (Bt). This regulation occurs through the ExuR transcription factor. However, galacturonic-acid is also sensed as a signal through ExuR to modulate the expression of the genes encoding a molecular syringe known as a type three secretion system (T3SS) leading to infectious colitis and inflammation. Galacturonic-acid moonlights as a nutrient and a signal directing the exquisite microbiota-pathogen relationships within the GI tract. Importantly, this work highlights that differential dietary sugar availability impacts the relationship between the microbiota and enteric pathogens, as well as disease outcomes.
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Affiliation(s)
- Angel G Jimenez
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Melissa Ellermann
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada.,Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Vanessa Sperandio
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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46
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Yu J, Lu Y. Carbon dioxide fixation by a hydrogen-oxidizing bacterium: Biomass yield, reversal respiratory quotient, stoichiometric equations and bioenergetics. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107369] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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47
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Xu X, Zhang H, Huang Y, Zhang Y, Wu C, Gao P, Teng Z, Luo X, Peng X, Wang X, Wang D, Pu J, Zhao H, Lu X, Lu S, Ye C, Dong Y, Lan R, Xu J. Beyond a Ribosomal RNA Methyltransferase, the Wider Role of MraW in DNA Methylation, Motility and Colonization in Escherichia coli O157:H7. Front Microbiol 2019; 10:2520. [PMID: 31798540 PMCID: PMC6863780 DOI: 10.3389/fmicb.2019.02520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
MraW is a 16S rRNA methyltransferase and plays a role in the fine-tuning of the ribosomal decoding center. It was recently found to contribute to the virulence of Staphylococcus aureus. In this study, we examined the function of MraW in Escherichia coli O157:H7 and found that the deletion of mraW led to decreased motility, flagellar production and DNA methylation. Whole-genome bisulfite sequencing showed a genome wide decrease of methylation of 336 genes and 219 promoters in the mraW mutant including flagellar genes. The methylation level of flagellar genes was confirmed by bisulfite PCR sequencing. Quantitative reverse transcription PCR results indicated that the transcription of these genes was also affected. MraW was furtherly observed to directly bind to the four flagellar gene sequences by electrophoretic mobility shift assay (EMSA). A common flexible motif in differentially methylated regions (DMRs) of promoters and coding regions of the four flagellar genes was identified. Reduced methylation was correlated with altered expression of 21 of the 24 genes tested. DNA methylation activity of MraW was confirmed by DNA methyltransferase activity assay in vitro and repressed by DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-aza). In addition, the mraW mutant colonized poorer than wild type in mice. We also found that the expression of mraZ in the mraW mutant was increased confirming the antagonistic effect of mraW on mraZ. In conclusion, mraW was found to be a DNA methylase and have a wide-ranging effect on E. coli O157:H7 including motility and virulence in vivo via genome wide methylation and mraZ antagonism.
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Affiliation(s)
- Xuefang Xu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Heng Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Ying Huang
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yuan Zhang
- China Institute of Veterinary Drug Control, Haidian, China
| | - Changde Wu
- College of Animal Sciences and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Pengya Gao
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,College of Animal Sciences and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhongqiu Teng
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xuelian Luo
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaojing Peng
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaoyuan Wang
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Dai Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Ji Pu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hongqing Zhao
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xuancheng Lu
- Laboratory Animal Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuangshuang Lu
- Laboratory Animal Center, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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48
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Kitamoto S, Alteri CJ, Rodrigues M, Nagao-Kitamoto H, Sugihara K, Himpsl SD, Bazzi M, Miyoshi M, Nishioka T, Hayashi A, Morhardt TL, Kuffa P, Grasberger H, El-Zaatari M, Bishu S, Ishii C, Hirayama A, Eaton KA, Dogan B, Simpson KW, Inohara N, Mobley HLT, Kao JY, Fukuda S, Barnich N, Kamada N. Dietary L-serine confers a competitive fitness advantage to Enterobacteriaceae in the inflamed gut. Nat Microbiol 2019; 5:116-125. [PMID: 31686025 PMCID: PMC6925351 DOI: 10.1038/s41564-019-0591-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/12/2019] [Indexed: 12/19/2022]
Abstract
Metabolic reprogramming is associated with the adaptation of host cells to the disease environment, such as inflammation and cancer. However, little is known about microbial metabolic reprogramming or the role it plays in regulating the fitness of commensal and pathogenic bacteria in the gut. Here, we report that intestinal inflammation reprograms the metabolic pathways of Enterobacteriaceae, such as Escherichia coli LF82, in the gut to adapt to the inflammatory environment. We found that E. coli LF82 shifts its metabolism to catabolize L-serine in the inflamed gut in order to maximize its growth potential. However, L-serine catabolism has a minimal effect on its fitness in the healthy gut. In fact, the absence of genes involved in L-serine utilization reduces the competitive fitness of E. coli LF82 and Citrobacter rodentium only during inflammation. The concentration of luminal L-serine is largely dependent on dietary intake. Accordingly, withholding amino acids from the diet markedly reduces their availability in the gut lumen. Hence, inflammation-induced blooms of E. coli LF82 are significantly blunted when amino acids-particularly L-serine-are removed from the diet. Thus, the ability to catabolize L-serine increases bacterial fitness and provides Enterobacteriaceae with a growth advantage against competitors in the inflamed gut.
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Affiliation(s)
- Sho Kitamoto
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Michael Rodrigues
- M2iSH, UMR1071 Inserm/University Clermont Auvergne, Clermont-Ferrand, France
| | - Hiroko Nagao-Kitamoto
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kohei Sugihara
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie D Himpsl
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Malak Bazzi
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mao Miyoshi
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Tatsuki Nishioka
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Atsushi Hayashi
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.,Research Laboratory, Miyarisan Pharmaceutical, Tokyo, Japan
| | - Tina L Morhardt
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.,Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Kuffa
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Helmut Grasberger
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mohamad El-Zaatari
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Shrinivas Bishu
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Chiharu Ishii
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Kathryn A Eaton
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Belgin Dogan
- College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - Naohiro Inohara
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Harry L T Mobley
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - John Y Kao
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Ebina, Japan.,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Nicolas Barnich
- M2iSH, UMR1071 Inserm/University Clermont Auvergne, Clermont-Ferrand, France
| | - Nobuhiko Kamada
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
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49
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Effects of gluconate on biomass improvement and light stress tolerance of Haematococcus pluvialis in mixotrophic culture. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101647] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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50
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Taylor MR, Flannigan KL, Rahim H, Mohamud A, Lewis IA, Hirota SA, Greenway SC. Vancomycin relieves mycophenolate mofetil-induced gastrointestinal toxicity by eliminating gut bacterial β-glucuronidase activity. SCIENCE ADVANCES 2019; 5:eaax2358. [PMID: 31457102 PMCID: PMC6685722 DOI: 10.1126/sciadv.aax2358] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/28/2019] [Indexed: 05/08/2023]
Abstract
Mycophenolate mofetil (MMF) is commonly prescribed and has proven advantages over other immunosuppressive drugs. However, frequent gastrointestinal side effects through an unknown mechanism limit its use. We have found that consumption of MMF alters the composition of the gut microbiota, selecting for bacteria expressing the enzyme β-glucuronidase (GUS) and leading to an up-regulation of GUS activity in the gut of mice and symptomatic humans. In the mouse, vancomycin eliminated GUS-expressing bacteria and prevented MMF-induced weight loss and colonic inflammation. Our work provides a mechanism for the toxicity associated with MMF and a future direction for the development of therapeutics.
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Affiliation(s)
- Michael R. Taylor
- Departments of Pediatrics and Cardiac Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kyle L. Flannigan
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Hannah Rahim
- Departments of Pediatrics and Cardiac Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Amina Mohamud
- Departments of Pediatrics and Cardiac Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ian A. Lewis
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Simon A. Hirota
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Steven C. Greenway
- Departments of Pediatrics and Cardiac Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Corresponding author.
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