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Hu Z, Chin Y, Yuan C, Ge Y, Hang Y, Wang D, Yao Q, Hu Y. The luxS deletion reduces the spoilage ability of Shewanella putrefaciens: An analysis focusing on quorum sensing and activated methyl cycle. Food Microbiol 2024; 120:104467. [PMID: 38431319 DOI: 10.1016/j.fm.2024.104467] [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: 11/13/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 03/05/2024]
Abstract
The luxS mutant strains of Shewanella putrefaciens (SHP) were constructed to investigate the regulations of gene luxS in spoilage ability. The potential regulations of AI-2 quorum sensing (QS) system and activated methyl cycle (AMC) were studied by analyzing the supplementation roles of key circulating substances mediated via luxS, including S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), methionine (Met), homocysteine (Hcy) and 4,5-dihydroxy-2,3-pentanedione (DPD). Growth experiments revealed that the luxS deletion led to certain growth limitations of SHP, which were associated with culture medium and exogenous additives. Meanwhile, the decreased biofilm formation and diminished hydrogen sulfide (H2S) production capacity of SHP were observed after luxS deletion. The relatively lower total volatile base nitrogen (TVB-N) contents and higher sensory scores of fish homogenate with luxS mutant strain inoculation also indicated the weaker spoilage-inducing effects after luxS deletion. However, these deficiencies could be offset with the exogenous supply of circulating substances mentioned above. Our findings suggested that the luxS deletion would reduce the spoilage ability of SHP, which was potentially attributed to the disorder of AMC and AI-2 QS system.
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Affiliation(s)
- Zhiheng Hu
- College of Food Science and Engineering, Hainan Tropical Ocean University, Yazhou Bay Innovation Institute, Marine Food Engineering Technology Research Center of Hainan Province, Collaborative Innovation Center of Marine Food Deep Processing, Sanya 572022, China; United Graduate School of Agricultural Sciences, Ueda 3-8-18, Morioka, Iwate 020-8550, Japan
| | - Yaoxian Chin
- College of Food Science and Engineering, Hainan Tropical Ocean University, Yazhou Bay Innovation Institute, Marine Food Engineering Technology Research Center of Hainan Province, Collaborative Innovation Center of Marine Food Deep Processing, Sanya 572022, China
| | - Chunhong Yuan
- Faculty of Agriculture, Iwate University, Ueda 3-8-18, Morioka, Iwate 020-8550, Japan; Agri-Innovation Center, Iwate University, Ueda 3-8-18, Morioka, Iwate 020-8550, Japan
| | - Yingliang Ge
- College of Food Science and Engineering, Hainan Tropical Ocean University, Yazhou Bay Innovation Institute, Marine Food Engineering Technology Research Center of Hainan Province, Collaborative Innovation Center of Marine Food Deep Processing, Sanya 572022, China
| | - Yuyu Hang
- College of Food Science and Engineering, Hainan Tropical Ocean University, Yazhou Bay Innovation Institute, Marine Food Engineering Technology Research Center of Hainan Province, Collaborative Innovation Center of Marine Food Deep Processing, Sanya 572022, China
| | - Dongxue Wang
- College of Food Science and Engineering, Hainan Tropical Ocean University, Yazhou Bay Innovation Institute, Marine Food Engineering Technology Research Center of Hainan Province, Collaborative Innovation Center of Marine Food Deep Processing, Sanya 572022, China
| | - Qian Yao
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Yaqin Hu
- College of Food Science and Engineering, Hainan Tropical Ocean University, Yazhou Bay Innovation Institute, Marine Food Engineering Technology Research Center of Hainan Province, Collaborative Innovation Center of Marine Food Deep Processing, Sanya 572022, China.
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Mok JH, Park DY, Han JC. Differential protein expression and metabolite profiling in glaucoma: Insights from a multi-omics analysis. Biofactors 2024. [PMID: 38818964 DOI: 10.1002/biof.2079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/04/2024] [Indexed: 06/01/2024]
Abstract
Various substances within the aqueous humor (AH) can directly or indirectly impact intraocular tissues associated with intraocular pressure (IOP), a critical factor in glaucoma development. This study aims to investigate individual changes in these AH substances and the interactions among altered components through a multi-omics approach. LC/MS analysis was conducted on AH samples from patients with exfoliation syndrome (XFS, n = 5), exfoliation glaucoma (XFG, n = 4), primary open-angle glaucoma (POAG, n = 11), and cataracts (control group, n = 7). Subsequently, differentially expressed proteins and metabolites among groups, alterations in their network interactions, and their biological functions were examined. Both data-independent acquisition and data-dependent acquisition methods were employed to analyze the AH proteome and metabolome, and the results were integrated for a comprehensive analysis. In the proteomics analysis, proteins upregulated in both the XFG and POAG groups were associated with lipid metabolism, complement activation, and extracellular matrix regulation. Metabolomic analysis highlighted significant changes in amino acids related to antioxidant processes in the glaucoma groups. Notably, VTN, APOA1, C6, and L-phenylalanine exhibited significant alterations in the glaucoma groups. Integration of individual omics analyses demonstrated that substances associated with inflammation and lipid metabolism, altered in the glaucoma groups, showed robust interactions within a complex network involving PLG, APOA1, and L-phenylalanine or C3, APOD, and L-valine. These findings offer valuable insights into the molecular mechanisms governing IOP regulation and may contribute to the development of new biomarkers for managing glaucoma.
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Affiliation(s)
- Jeong-Hun Mok
- Department of Medical Device Management and Research, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Do Young Park
- Department of Ophthalmology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong Chul Han
- Department of Medical Device Management and Research, SAIHST, Sungkyunkwan University, Seoul, Korea
- Department of Ophthalmology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Ma D, Du G, Fang H, Li R, Zhang D. Advances and prospects in microbial production of biotin. Microb Cell Fact 2024; 23:135. [PMID: 38735926 PMCID: PMC11089781 DOI: 10.1186/s12934-024-02413-1] [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: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024] Open
Abstract
Biotin, serving as a coenzyme in carboxylation reactions, is a vital nutrient crucial for the natural growth, development, and overall well-being of both humans and animals. Consequently, biotin is widely utilized in various industries, including feed, food, and pharmaceuticals. Despite its potential advantages, the chemical synthesis of biotin for commercial production encounters environmental and safety challenges. The burgeoning field of synthetic biology now allows for the creation of microbial cell factories producing bio-based products, offering a cost-effective alternative to chemical synthesis for biotin production. This review outlines the pathway and regulatory mechanism involved in biotin biosynthesis. Then, the strategies to enhance biotin production through both traditional chemical mutagenesis and advanced metabolic engineering are discussed. Finally, the article explores the limitations and future prospects of microbial biotin production. This comprehensive review not only discusses strategies for biotin enhancement but also provides in-depth insights into systematic metabolic engineering approaches aimed at boosting biotin production.
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Affiliation(s)
- Donghan Ma
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Guangqing Du
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Rong Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Tan B, Xiao D, Wang J, Tan B. The Roles of Polyamines in Intestinal Development and Function in Piglets. Animals (Basel) 2024; 14:1228. [PMID: 38672376 PMCID: PMC11047586 DOI: 10.3390/ani14081228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
The gastrointestinal tract plays crucial roles in the digestion and absorption of nutrients, as well as in maintenance of a functional barrier. The development and maturation of the intestine is important for piglets to maintain optimal growth and health. Polyamines are necessary for the proliferation and growth of enterocytes, which play a key role in differentiation, migration, remodeling and integrity of the intestinal mucosa after injury. This review elaborates the development of the structure and function of the intestine of piglets during embryonic, suckling and weaning periods, the utilization and metabolism of polyamines in the intestine, as well as the role of polyamines in intestinal development and mucosal repair. The nutritional intervention to improve intestinal development and functions by modulating polyamine metabolism in piglets is also put forward. These results may help to promote the adaption to weaning in pigs and provide useful information for the development and health of piglets.
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Affiliation(s)
- Bihui Tan
- Key Laboratory for Quality Regulation of Livestock and Poultry Products of Hunan Province, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (B.T.); (D.X.); (J.W.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Dingfu Xiao
- Key Laboratory for Quality Regulation of Livestock and Poultry Products of Hunan Province, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (B.T.); (D.X.); (J.W.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Jing Wang
- Key Laboratory for Quality Regulation of Livestock and Poultry Products of Hunan Province, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (B.T.); (D.X.); (J.W.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Bi’e Tan
- Key Laboratory for Quality Regulation of Livestock and Poultry Products of Hunan Province, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (B.T.); (D.X.); (J.W.)
- Yuelushan Laboratory, Changsha 410128, China
- Hunan Linxi Biological Technology Co., Ltd. Expert Workstation, Changsha 410202, China
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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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Hara T, Sakanaka A, Lamont RJ, Amano A, Kuboniwa M. Interspecies metabolite transfer fuels the methionine metabolism of Fusobacterium nucleatum to stimulate volatile methyl mercaptan production. mSystems 2024; 9:e0076423. [PMID: 38289043 PMCID: PMC10878106 DOI: 10.1128/msystems.00764-23] [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: 08/08/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024] Open
Abstract
The major oral odor compound methyl mercaptan (CH3SH) is strongly associated with halitosis and periodontitis. CH3SH production stems from the metabolism of polymicrobial communities in periodontal pockets and on the tongue dorsum. However, understanding of CH3SH-producing oral bacteria and their interactions is limited. This study aimed to investigate CH3SH production by major oral bacteria and the impact of interspecies interactions on its generation. Using a newly constructed large-volume anaerobic noncontact coculture system, Fusobacterium nucleatum was found to be a potent producer of CH3SH, with that production stimulated by metabolic interactions with Streptococcus gordonii, an early dental plaque colonizer. Furthermore, analysis of extracellular amino acids using an S. gordonii arginine-ornithine antiporter (ArcD) mutant demonstrated that ornithine excreted from S. gordonii is a key contributor to increased CH3SH production by F. nucleatum. Further study with 13C, 15N-methionine, as well as gene expression analysis, revealed that ornithine secreted by S. gordonii increased the demand for methionine through accelerated polyamine synthesis by F. nucleatum, leading to elevated methionine pathway activity and CH3SH production. Collectively, these findings suggest that interaction between S. gordonii and F. nucleatum plays a key role in CH3SH production, providing a new insight into the mechanism of CH3SH generation in oral microbial communities. A better understanding of the underlying interactions among oral bacteria involved in CH3SH generation can lead to the development of more appropriate prophylactic approaches to treat halitosis and periodontitis. An intervention approach like selectively disrupting this interspecies network could also offer a powerful therapeutic strategy.IMPORTANCEHalitosis can have a significant impact on the social life of affected individuals. Among oral odor compounds, CH3SH has a low olfactory threshold and halitosis is a result of its production. Recently, there has been a growing interest in the collective properties of oral polymicrobial communities, regarded as important for the development of oral diseases, which are shaped by physical and metabolic interactions among community participants. However, it has yet to be investigated whether interspecies interactions have an impact on the production of volatile compounds, leading to the development of halitosis. The present findings provide mechanistic insights indicating that ornithine, a metabolite excreted by Streptococcus gordonii, promotes polyamine synthesis by Fusobacterium nucleatum, resulting in a compensatory increase in demand for methionine, which results in elevated methionine pathway activity and CH3SH production. Elucidation of the mechanisms related to CH3SH production is expected to lead to the development of new strategies for managing halitosis.
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Affiliation(s)
- Takeshi Hara
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- Advanced Technology Institute, Mandom Corporation, Osaka, Japan
| | - Akito Sakanaka
- Department of Preventive Density, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - Richard J. Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, Kentucky, USA
| | - Atsuo Amano
- Department of Preventive Density, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - Masae Kuboniwa
- Department of Preventive Density, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
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Polidore ALA, Caserio AD, Zhu L, Metcalf WW. Complete Biochemical Characterization of Pantaphos Biosynthesis Highlights an Unusual Role for a SAM-Dependent Methyltransferase. Angew Chem Int Ed Engl 2024; 63:e202317262. [PMID: 38141166 PMCID: PMC10873477 DOI: 10.1002/anie.202317262] [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: 11/13/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/25/2023]
Abstract
Pantaphos is small molecule virulence factor made by the plant pathogen Pantoea ananatis. An 11 gene operon, designated hvr for high virulence, is required for production of this phosphonic acid natural product, but the metabolic steps used in its production have yet to be established. Herein, we determine the complete biosynthetic pathway using a combination of bioinformatics, in vitro biochemistry and in vivo heterologous expression. Only 6 of the 11 hvr genes are needed to produce pantaphos, while a seventh is likely to be required for export. Surprisingly, the pathway involves a series of O-methylated intermediates, which are then hydrolyzed to produce the final product. The methylated intermediates are produced by an irreversible S-adenosylmethione (SAM)-dependent methyltransferase that is required to drive a thermodynamically unfavorable dehydration in the preceding step, a function not previously attributed to members of this enzyme class. Methylation of pantaphos by the same enzyme is also likely to limit its toxicity in the producing organism. The pathway also involves a novel flavin-dependent monooxygenase that differs from homologous proteins due to its endogenous flavin-reductase activity. Heterologous production of pantaphos by Escherichia coli strains expressing the minimal gene set strongly supports the in vitro biochemical data.
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Affiliation(s)
- Alexander L A Polidore
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin, Urbana, IL 61874, USA
| | - Angelica D Caserio
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin, Urbana, IL 61874, USA
| | - Lingyang Zhu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Ave, Urbana, IL 61874, USA
| | - William W Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin, Urbana, IL 61874, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61874, USA
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Simpson CA, Celentano Z, McKinlay JB, Nadell CD, van Kessel JC. Bacterial quorum sensing controls carbon metabolism to optimize growth in changing environmental conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.21.576522. [PMID: 38328067 PMCID: PMC10849521 DOI: 10.1101/2024.01.21.576522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Bacteria sense population density via the cell-cell communication system called quorum sensing (QS). Some QS-regulated phenotypes ( e.g. , secreted enzymes, chelators), are public goods exploitable by cells that stop producing them. We uncovered a phenomenon in which Vibrio cells optimize expression of the methionine and tetrahydrofolate (THF) synthesis genes via QS. Strains that are genetically 'locked' at high cell density grow slowly in minimal glucose media and suppressor mutants accumulate via inactivating-mutations in metF (methylenetetrahydrofolate reductase) and luxR (the master QS transcriptional regulator). Methionine/THF synthesis genes are repressed at low cell density when glucose is plentiful and are de-repressed by LuxR at high cell density as glucose becomes limiting. In mixed cultures, QS mutant strains initially co-exist with wild-type, but as glucose is depleted, wild-type outcompetes the QS mutants. Thus, QS regulation of methionine/THF synthesis is a fitness benefit that links private and public goods within the QS regulon, preventing accumulation of QS-defective mutants.
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Dai J, Luo W, Hu F, Li S. In vitro inhibition of Pseudomonas aeruginosa PAO1 biofilm formation by DZ2002 through regulation of extracellular DNA and alginate production. Front Cell Infect Microbiol 2024; 13:1333773. [PMID: 38268790 PMCID: PMC10806038 DOI: 10.3389/fcimb.2023.1333773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Introduction Pseudomonas aeruginosa (P. aeruginosa) is a common pathogen associated with biofilm infections, which can lead to persistent infections. Therefore, there is an urgent need to develop new anti-biofilm drugs. DZ2002 is a reversible inhibitor that targets S-adenosylhomocysteine hydrolase and possesses anti-inflammatory and immune-regulatory activities. However, its anti-biofilm activity has not been reported yet. Methods and results Therefore, we investigated the effect of DZ2002 on P. aeruginosa PAO1 biofilm formation by crystal violet staining (CV), real-time quantitative polymerase chain reaction (RT-qPCR) and confocal laser scanning microscopy (CLSM). The results indicated that although DZ2002 didn't affect the growth of planktonic PAO1, it could significantly inhibit the formation of mature biofilms. During the inhibition of biofilm formation by DZ2002, there was a parallel decrease in the synthesis of alginate and the expression level of alginate genes, along with a weakening of swarming motility. However, these results were unrelated to the expression of lasI, lasR, rhII, rhIR. Additionally, we also found that after treatment with DZ2002, the biofilms and extracellular DNA content of PAO1 were significantly reduced. Molecular docking results further confirmed that DZ2002 had a strong binding affinity with the active site of S-adenosylhomocysteine hydrolase (SahH) of PAO1. Discussion In summary, our results indicated that DZ2002 may interact with SahH in PAO1, inhibiting the formation of mature biofilms by downregulating alginate synthesis, extracellular DNA production and swarming motility. These findings demonstrate the potential value of DZ2002 in treating biofilm infections associated with P. aeruginosa.
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Affiliation(s)
- Jiaze Dai
- Medical Laboratory Center, Affiliated Hospital of Guangdong Medical University, Zhan Jiang, Guang Dong, China
| | - Wenying Luo
- Medical Laboratory Center, Affiliated Hospital of Guangdong Medical University, Zhan Jiang, Guang Dong, China
| | - Fei Hu
- Medical Laboratory Center, Affiliated Hospital of Guangdong Medical University, Zhan Jiang, Guang Dong, China
| | - Si Li
- General Medicine, Clinical Medicine, Kangda College of Nanjing Medical University, LianYun Gang, Jiang Su, China
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10
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Salvail H, Balaji A, Roth A, Breaker RR. A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine. Cell Rep 2023; 42:113571. [PMID: 38096053 PMCID: PMC10853860 DOI: 10.1016/j.celrep.2023.113571] [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: 09/12/2023] [Revised: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
Natural polyamines such as spermidine and spermine cations have characteristics that make them highly likely to be sensed by riboswitches, such as their general affinity to polyanionic RNA and their broad contributions to cell physiology. Despite previous claims that polyamine riboswitches exist, evidence of their biological functions has remained unconvincing. Here, we report that rare variants of bacterial S-adenosylmethionine-I (SAM-I) riboswitches reject SAM and have adapted to selectively sense spermidine. These spermidine-sensing riboswitch variants are associated with genes whose protein products are directly involved in the production of spermidine and other polyamines. Biochemical and genetic assays demonstrate that representatives of this riboswitch class robustly function as genetic "off" switches, wherein spermidine binding causes premature transcription termination to suppress the expression of polyamine biosynthetic genes. These findings confirm the existence of natural spermidine-sensing riboswitches in bacteria and expand the list of variant riboswitch classes that have adapted to bind different ligands.
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Affiliation(s)
- Hubert Salvail
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Aparaajita Balaji
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA
| | - Adam Roth
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103, USA.
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11
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Cai M, Liu Z, Zhao Z, Wu H, Xu M, Rao Z. Microbial production of L-methionine and its precursors using systems metabolic engineering. Biotechnol Adv 2023; 69:108260. [PMID: 37739275 DOI: 10.1016/j.biotechadv.2023.108260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/11/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
L-methionine is an essential amino acid with versatile applications in food, feed, cosmetics and pharmaceuticals. At present, the production of L-methionine mainly relies on chemical synthesis, which conflicts with the concern over serious environmental problems and sustainable development goals. In recent years, microbial production of natural products has been amply rewarded with the emergence and rapid development of system metabolic engineering. However, efficient L-methionine production by microbial fermentation remains a great challenge due to its complicated biosynthetic pathway and strict regulatory mechanism. Additionally, the engineered production of L-methionine precursors, L-homoserine, O-succinyl-L-homoserine (OSH) and O-acetyl-L-homoserine (OAH), has also received widespread attention because they can be catalyzed to L-methionine via a high-efficiently enzymatic reaction in vitro, which is also a promising alternative to chemical route. This review provides a comprehensive overview on the recent advances in the microbial production of L-methionine and its precursors, highlighting the challenges and potential solutions for developing L-methionine microbial cell factories from the perspective of systems metabolic engineering, aiming to offer guidance for future engineering.
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Affiliation(s)
- Mengmeng Cai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhifei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhenqiang Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Hongxuan Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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12
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Xiao L, An Q, Xu R, Li C, Zhang C, Ma K, Ji F, Azarpazhooh E, Ajami M, Rui X, Li W. Roles of luxS in regulation of probiotic characteristics and inhibition of pathogens in Lacticaseibacillus paracasei S-NB. Microb Pathog 2023; 184:106379. [PMID: 37802157 DOI: 10.1016/j.micpath.2023.106379] [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: 08/22/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023]
Abstract
Lactic acid bacteria (LAB) have excellent tolerance to the gastrointestinal environment and high adhesion ability to intestinal epithelial cells, which could be closely related to the LuxS/AI-2 Quorum sensing (QS) system. Here, the crucial enzymes involved in the synthesis of AI-2 was analyzed in Lacticaseibacillus paracasei S-NB, and the luxS deletion mutant was constructed by homologous recombination based on the Cre-lox system. Afterwards, the effect of luxS gene on the probiotic activities in L. paracasei S-NB was investigated. Notably, the tolerance of simulated gastrointestinal digestion, AI-2 production, ability of auto-aggregation and biofilm formation significantly decreased (p < 0.05 for all) in the S-NB△luxS mutant. Compared to the wild-type S-NB, the degree of reduction in the relative transcriptional level of the biofilm -related genes in Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 25923 was diminished when co-cultured with S-NB△luxS. Furthermore, the inhibitory effect of S-NB△luxS on the adhesion (competition, exclusion and displacement) of E. coli ATCC 25922 and S. aureus ATCC 25923 to Caco-2 cells markedly decreased. Therefore, comprehensive analysis of the role by luxS provides an insight into the LuxS/AI-2 QS system of L. paracasei S-NB in the regulation of strain characteristics and inhibition of pathogens.
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Affiliation(s)
- Luyao Xiao
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Qi An
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Ruiqi Xu
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Chen Li
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Changliang Zhang
- Jiangsu New-Bio Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China; Jiangsu Biodep Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China
| | - Kai Ma
- Jiangsu New-Bio Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China; Jiangsu Biodep Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China
| | - Feng Ji
- Jiangsu New-Bio Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China; Jiangsu Biodep Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China
| | - Elham Azarpazhooh
- Khorasan Razavi Agricultural and Natural Resources Research and Education Center, AREEO, Iran
| | - Marjan Ajami
- National Nutrition and Food Technology Research Institute, School of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Xin Rui
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Wei Li
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
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13
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Muok AR, Kurniyati K, Cassidy CK, Olsthoorn FA, Ortega DR, Mabrouk AS, Li C, Briegel A. A new class of protein sensor links spirochete pleomorphism, persistence, and chemotaxis. mBio 2023; 14:e0159823. [PMID: 37607060 PMCID: PMC10653840 DOI: 10.1128/mbio.01598-23] [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: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 08/24/2023] Open
Abstract
IMPORTANCE A new class of bacterial protein sensors monitors intracellular levels of S-adenosylmethionine to modulate cell morphology, chemotaxis, and biofilm formation. Simultaneous regulation of these behaviors enables bacterial pathogens to survive within their niche. This sensor, exemplified by Treponema denticola CheWS, is anchored to the chemotaxis array and its sensor domain is located below the chemotaxis rings. This position may allow the sensor to directly interact with the chemotaxis histidine kinase CheA. Collectively, these data establish a critical role of CheWS in pathogenesis and further illustrate the impact of studying non-canonical chemotaxis proteins.
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Affiliation(s)
- A. R. Muok
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - K. Kurniyati
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, Virginia, USA
| | - C. K. Cassidy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - F. A. Olsthoorn
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - D. R. Ortega
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - A. Sidi Mabrouk
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - C. Li
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, Virginia, USA
| | - A. Briegel
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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14
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Brown M, Schramm VL. Decreased Transition-State Analogue Affinity in Isotopically Heavy MTAN with Increased Catalysis. Biochemistry 2023; 62:2928-2933. [PMID: 37788145 PMCID: PMC10636763 DOI: 10.1021/acs.biochem.3c00434] [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] [Indexed: 10/05/2023]
Abstract
5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase from Helicobacter pylori (HpMTAN) demonstrated faster chemistry when expressed as an isotopically heavy protein, with 2H, 13C, and 15N replacing the bulk of normal isotopes. The inverse heavy enzyme isotope effect has been attributed to improved enzyme-reactant interactions causing more frequent transition-state formation ( Proc. Natl. Acad. Sci. U.S.A. 2021, 118, e2109118118). Transition-state analogues stabilize the transient dynamic geometry of the transition state and inform on transition-state dynamics. Here, a slow-onset, tight-binding transition-state analogue of HpMTAN is characterized with heavy and light enzymes. Dissociation constants for the initial encounter complex (Ki) and for the tightly bound complex after slow-onset inhibition (Ki*) with hexylthio-DADMe-Immucillin-A (HTDIA) gave Ki values for light and heavy HpMTAN = 52 ± 10 and 85 ± 13 pM and Ki* values = 5.9 ± 0.3 and 10.0 ± 1.2 pM, respectively. HTDIA dissociates from heavy HpMTAN at 0.063 ± 0.002 min-1, faster than that from light HpMTAN at 0.032 ± 0.004 min-1. These values are consistent with transition-state formation by an improved catalytic site dynamic search and inconsistent with catalytic efficiency proportional to tight binding of the transition state.
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Affiliation(s)
- Morais Brown
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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15
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Li H, Mo P, Zhang J, Xie Z, Liu X, Chen H, Yang L, Liu M, Zhang H, Wang P, Zhang Z. Methionine biosynthesis enzyme MoMet2 is required for rice blast fungus pathogenicity by promoting virulence gene expression via reducing 5mC modification. PLoS Genet 2023; 19:e1010927. [PMID: 37733784 PMCID: PMC10547190 DOI: 10.1371/journal.pgen.1010927] [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: 04/12/2023] [Revised: 10/03/2023] [Accepted: 08/20/2023] [Indexed: 09/23/2023] Open
Abstract
The emergence of fungicide resistance severely threatens crop production by limiting the availability and application of established fungicides. Therefore, it is urgent to identify new fungicidal targets for controlling plant diseases. Here, we characterized the function of a conserved homoserine O-acetyltransferase (HOA) from the rice blast fungus Magnaporthe oryzae that could serve as the candidate antifungal target. Deletion of the MoMET2 and MoCYS2 genes encoding HOAs perturbed the biosynthesis of methionine and S-adenyl methionine, a methyl group donor for epigenetic modifications, and severely attenuated the development and virulence of M. oryzae. The ∆Momet2 mutant is significantly increased in 5-methylcytosine (5mC) modification that represses the expression of genes required for pathogenicity, including MoGLIK and MoCDH-CYT. We further showed that host-induced gene silencing (HIGS) targeting MoMET2 and MoCYS2 effectively controls rice blasts. Our studies revealed the importance of HOA in the development and virulence of M. oryzae, which suggests the potential feasibility of HOA as new targets for novel anti-rice blast measurements.
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Affiliation(s)
- Huimin Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Pengcheng Mo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Jun Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Zhuoer Xie
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xinyu Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Han Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Leiyun Yang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Muxing Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Ping Wang
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
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16
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Becker CC, Weber L, Zgliczynski B, Sullivan C, Sandin S, Muller E, Clark AS, Kido Soule MC, Longnecker K, Kujawinski EB, Apprill A. Microorganisms and dissolved metabolites distinguish Florida's Coral Reef habitats. PNAS NEXUS 2023; 2:pgad287. [PMID: 37719750 PMCID: PMC10504872 DOI: 10.1093/pnasnexus/pgad287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/24/2023] [Indexed: 09/19/2023]
Abstract
As coral reef ecosystems experience unprecedented change, effective monitoring of reef features supports management, conservation, and intervention efforts. Omic techniques show promise in quantifying key components of reef ecosystems including dissolved metabolites and microorganisms that may serve as invisible sensors for reef ecosystem dynamics. Dissolved metabolites are released by reef organisms and transferred among microorganisms, acting as chemical currencies and contributing to nutrient cycling and signaling on reefs. Here, we applied four omic techniques (taxonomic microbiome via amplicon sequencing, functional microbiome via shotgun metagenomics, targeted metabolomics, and untargeted metabolomics) to waters overlying Florida's Coral Reef, as well as microbiome profiling on individual coral colonies from these reefs to understand how microbes and dissolved metabolites reflect biogeographical, benthic, and nutrient properties of this 500-km barrier reef. We show that the microbial and metabolite omic approaches each differentiated reef habitats based on geographic zone. Further, seawater microbiome profiling and targeted metabolomics were significantly related to more reef habitat characteristics, such as amount of hard and soft coral, compared to metagenomic sequencing and untargeted metabolomics. Across five coral species, microbiomes were also significantly related to reef zone, followed by species and disease status, suggesting that the geographic water circulation patterns in Florida also impact the microbiomes of reef builders. A combination of differential abundance and indicator species analyses revealed metabolite and microbial signatures of specific reef zones, which demonstrates the utility of these techniques to provide new insights into reef microbial and metabolite features that reflect broader ecosystem processes.
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Affiliation(s)
- Cynthia C Becker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- Biological Oceanography, Massachusetts Institute of Technology-Woods Hole Oceanographic Institution Joint Program in Oceanography/Applied Ocean Science and Engineering,Cambridge, MA 02139, USA
| | - Laura Weber
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Brian Zgliczynski
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Chris Sullivan
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Stuart Sandin
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Erinn Muller
- Elizabeth Moore International Center for Coral Reef Research and Restoration, Mote Marine Laboratory, Summerland Key, FL 33042, USA
- Coral Health and Disease Program, Mote Marine Laboratory, Sarasota, FL 34236, USA
| | - Abigail S Clark
- Elizabeth Moore International Center for Coral Reef Research and Restoration, Mote Marine Laboratory, Summerland Key, FL 33042, USA
- Marine Science and Technology Department, The College of the Florida Keys, Key West, FL 33040, USA
| | - Melissa C Kido Soule
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Krista Longnecker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Elizabeth B Kujawinski
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Amy Apprill
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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17
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Huening KA, Groves JT, Wildenthal JA, Tabita FR, North JA. Utilization of 5'-deoxy-nucleosides as Growth Substrates by Extraintestinal Pathogenic E. coli via the Dihydroxyacetone Phosphate Shunt. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552779. [PMID: 37609188 PMCID: PMC10441430 DOI: 10.1101/2023.08.10.552779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
All organisms utilize S-adenosyl-l-methionine (SAM) as a key co-substrate for methylation of biological molecules, synthesis of polyamines, and radical SAM reactions. When these processes occur, 5'-deoxy-nucleosides are formed as byproducts such as S-adenosyl-l-homocysteine (SAH), 5'-methylthioadenosine (MTA), and 5'-deoxyadenosine (5dAdo). One of the most prevalent pathways found in bacteria for the metabolism of MTA and 5dAdo is the DHAP shunt, which converts these compounds into dihydroxyacetone phosphate (DHAP) and 2-methylthioacetaldehyde or acetaldehyde, respectively. Previous work has shown that the DHAP shunt can enable methionine synthesis from MTA or serve as an MTA and 5dAdo detoxification pathway. Here we show that in Extraintestinal Pathogenic E. coil (ExPEC), the DHAP shunt serves none of these roles in any significant capacity, but rather physiologically functions as an assimilation pathway for use of MTA and 5dAdo as growth substrates. This is further supported by the observation that when MTA is the substrate for the ExPEC DHAP shunt, the sulfur components is not significantly recycled back to methionine, but rather accumulates as 2-methylthioethanol, which is slowly oxidized non-enzymatically under aerobic conditions. While the pathway is active both aerobically and anaerobically, it only supports aerobic ExPEC growth, suggesting that it primarily functions in oxygenic extraintestinal environments like blood and urine versus the predominantly anoxic gut. This reveals a heretofore overlooked role of the DHAP shunt in carbon assimilation 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.
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Affiliation(s)
| | - Joshua T. Groves
- The Ohio State University Department of Microbiology, Columbus, OH, 43210
| | - John A. Wildenthal
- The Ohio State University Department of Microbiology, Columbus, OH, 43210
| | - F. Robert Tabita
- The Ohio State University Department of Microbiology, Columbus, OH, 43210
| | - Justin A. North
- The Ohio State University Department of Microbiology, Columbus, OH, 43210
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18
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Rauthan K, Joshi S, Kumar L, Goel D, Kumar S. Functional annotation of uncharacterized proteins from Fusobacterium nucleatum: identification of virulence factors. Genomics Inform 2023; 21:e21. [PMID: 37415454 PMCID: PMC10326533 DOI: 10.5808/gi.22065] [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: 09/29/2022] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 07/08/2023] Open
Abstract
Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as "Uncharacterized." Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.
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Affiliation(s)
- Kanchan Rauthan
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Saranya Joshi
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Lokesh Kumar
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Divya Goel
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
| | - Sudhir Kumar
- Department of Biotechnology, H.N.B. Garhwal University, Srinagar Garhwal, Uttarakhnd 246174, India
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19
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Sadeeshkumar H, Balaji A, Sutherland AG, Mootien S, Anthony KG, Breaker RR. Screening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch. Anal Biochem 2023; 666:115047. [PMID: 36682579 PMCID: PMC11149561 DOI: 10.1016/j.ab.2023.115047] [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: 10/21/2022] [Revised: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023]
Abstract
Due to the emergence of multidrug resistant pathogens, it is imperative to identify new targets for antibiotic drug discovery. The S-adenosylhomocysteine (SAH) nucleosidase enzyme is a promising target for antimicrobial drug development due to its critical functions in multiple bacterial processes including recycling of toxic byproducts of S-adenosylmethionine (SAM)-mediated reactions and producing the precursor of the universal quorum sensing signal, autoinducer-2 (AI-2). Riboswitches are structured RNA elements typically used by bacteria to precisely monitor and respond to changes in essential bacterial processes, including metabolism. Natural riboswitches fused to a reporter gene can be exploited to detect changes in metabolism or in physiological signaling. We performed a high-throughput screen (HTS) using an SAH-riboswitch controlled β-galactosidase reporter gene in Escherichia coli to discover small molecules that inhibit SAH recycling. We demonstrate that the assay strategy using SAH riboswitches to detect the effects of SAH nucleosidase inhibitors can quickly identify compounds that penetrate the barriers of Gram-negative bacterial cells and perturb pathways involving SAH.
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Affiliation(s)
- Harini Sadeeshkumar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8103, USA
| | - Aparaajita Balaji
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8103, USA
| | | | | | - Karen G Anthony
- L2 Diagnostics, LLC, 300 George Street, New Haven, CT, 06511, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8103, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520-8103, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520-8103, USA.
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20
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Patel R, Soni M, Soyantar B, Shivangi S, Sutariya S, Saraf M, Goswami D. A clash of quorum sensing vs quorum sensing inhibitors: an overview and risk of resistance. Arch Microbiol 2023; 205:107. [PMID: 36881156 DOI: 10.1007/s00203-023-03442-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 03/08/2023]
Abstract
Indiscriminate use of antibiotics to treat microbial pathogens has caused emergence of multiple drug resistant strains. Most infectious diseases are caused by microbes that are capable of intercommunication using signaling molecules, which is known as quorum sensing (QS). Such pathogens express their pathogenicity through various QS-regulated virulence factors. Interference of QS could lead to decisive results in controlling such pathogenicity. Hence, QS inhibition has become an attractive new approach for the development of novel drugs. Many quorum sensing inhibitors (QSIs) of diverse origins have been reported. It is imperative that more such anti-QS compounds be found and studied, as they have significant effect on microbial pathogenicity. This review attempts to give a brief account of QS mechanism, its inhibition and describes some compounds with anti-QS potential. Also discussed is the possibility of emergence of quorum sensing resistance.
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Affiliation(s)
- Rohit Patel
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Mansi Soni
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Bilv Soyantar
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Suruchi Shivangi
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Swati Sutariya
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Meenu Saraf
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Dweipayan Goswami
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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21
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Cao LY, Liu CG, Yang SH, Bai FW. Regulation of biofilm formation in Zymomonas mobilis to enhance stress tolerance by heterologous expression of pfs and luxS. Front Bioeng Biotechnol 2023; 11:1130405. [PMID: 36845188 PMCID: PMC9945106 DOI: 10.3389/fbioe.2023.1130405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
Zymomonas mobilis is a potential alternative of Saccharomyces cerevisiae to produce cellulosic ethanol with strengths in cofactor balance, but its lower tolerance to inhibitors in the lignocellulosic hydrolysate restricts the application. Although biofilm can improve bacteria stress tolerance, regulating biofilm formation in Z. mobilis is still a challenge. In this work, we constructed a pathway by heterologous expressing pfs and luxS from Escherichia coli in Z. mobilis to produce AI-2 (autoinducer 2), a universal quorum-sensing signal molecule, to control cell morphology for enhancing stress tolerance. Unexpectedly, the results suggested that neither endogenous AI-2 nor exogenous AI-2 promoted biofilm formation, while heterologous expression of pfs can significantly raise biofilm. Therefore, we proposed that the main factor in assisting biofilm formation was the product accumulated due to heterologous expression of pfs, like methylated DNA. Consequently, ZM4::pfs produced more biofilm, which presented an enhanced tolerance to acetic acid. All these findings provide a novel strategy to improve the stress tolerance of Z. mobilis by enhancing biofilm formation for efficient production of lignocellulosic ethanol and other value-added chemical products.
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Affiliation(s)
- Lian-Ying Cao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Chen-Guang Liu,
| | - Shi-Hui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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22
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Ramić D, Jug B, Šimunović K, Tušek Žnidarič M, Kunej U, Toplak N, Kovač M, Fournier M, Jamnik P, Smole Možina S, Klančnik A. The Role of luxS in Campylobacter jejuni Beyond Intercellular Signaling. Microbiol Spectr 2023; 11:e0257222. [PMID: 36722966 PMCID: PMC10100756 DOI: 10.1128/spectrum.02572-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/07/2023] [Indexed: 02/02/2023] Open
Abstract
The full role of the luxS gene in the biological processes, such as essential amino acid synthesis, nitrogen and pyruvate metabolism, and flagellar assembly, of Campylobacter jejuni has not been clearly described to date. Therefore, in this study, we used a comprehensive approach at the cellular and molecular levels, including transcriptomics and proteomics, to investigate the key role of the luxS gene and compared C. jejuni 11168ΔluxS (luxS mutant) and C. jejuni NCTC 11168 (wild type) strains. Transcriptomic analysis of the luxS mutant grown under optimal conditions revealed upregulation of luxS mutant metabolic pathways when normalized to wild type, including oxidative phosphorylation, carbon metabolism, citrate cycle, biosynthesis of secondary metabolites, and biosynthesis of various essential amino acids. Interestingly, induction of these metabolic pathways was also confirmed by proteomic analysis, indicating their important role in energy production and the growth of C. jejuni. In addition, genes important for the stress response of C. jejuni, including nutrient starvation and oxidative stress, were upregulated. This was also evident in the better survival of the luxS mutant under starvation conditions than the wild type. At the molecular level, we confirmed that metabolic pathways were upregulated under optimal conditions in the luxS mutant, including those important for the biosynthesis of several essential amino acids. This also modulated the utilization of various carbon and nitrogen sources, as determined by Biolog phenotype microarray analysis. In summary, transcriptomic and proteomic analysis revealed key biological differences in tricarboxylic acid (TCA) cycle, pyruvate, nitrogen, and thiamine metabolism as well as lipopolysaccharide biosynthesis in the luxS mutant. IMPORTANCE Campylobacter jejuni is the world's leading foodborne bacterial pathogen of gastrointestinal disease in humans. C. jejuni is a fastidious but widespread organism and the most frequently reported zoonotic pathogen in the European Union since 2005. This led us to believe that C. jejuni, which is highly sensitive to stress factors (starvation and oxygen concentration) and has a low growth rate, benefits significantly from the luxS gene. The role of this gene in the life cycle of C. jejuni is well known, and the expression of luxS regulates many phenotypes, including motility, biofilm formation, host colonization, virulence, autoagglutination, cellular adherence and invasion, oxidative stress, and chemotaxis. Surprisingly, this study confirmed for the first time that the deletion of the luxS gene strongly affects the central metabolic pathway of C. jejuni, which improves its survival, showing its role beyond the intercellular signaling system.
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Affiliation(s)
- Dina Ramić
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Jug
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Katarina Šimunović
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and System Biology, National institute of Biology, Ljubljana, Slovenia
| | - Urban Kunej
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | | | - Marjorie Fournier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Polona Jamnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sonja Smole Možina
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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23
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Zheng L, Song Q, Xu X, Shen X, Li C, Li H, Chen H, Ren A. Structure-based insights into recognition and regulation of SAM-sensing riboswitches. SCIENCE CHINA. LIFE SCIENCES 2023; 66:31-50. [PMID: 36459353 DOI: 10.1007/s11427-022-2188-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/17/2022] [Indexed: 12/03/2022]
Abstract
Riboswitches are highly conserved RNA elements that located in the 5'-UTR of mRNAs, which undergo real-time structure conformational change to achieve the regulation of downstream gene expression by sensing their cognate ligands. S-adenosylmethionine (SAM) is a ubiquitous methyl donor for transmethylation reactions in all living organisms. SAM riboswitch is one of the most abundant riboswitches that bind to SAM with high affinity and selectivity, serving as regulatory modules in multiple metabolic pathways. To date, seven SAM-specific riboswitch classes that belong to four families, one SAM/SAH riboswitch and one SAH riboswitch have been identified. Each SAM riboswitch family has a well-organized tertiary core scaffold to support their unique ligand-specific binding pocket. In this review, we summarize the current research progress on the distribution, structure, ligand recognition and gene regulation mechanism of these SAM-related riboswitch families, and further discuss their evolutionary prospects and potential applications.
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Affiliation(s)
- Luqian Zheng
- Department of Gastroenterology, Department of Cardiology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.,The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Qianqian Song
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Xiaochen Xu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Xin Shen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Chunyan Li
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Hongcheng Li
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Aiming Ren
- Department of Gastroenterology, Department of Cardiology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China. .,Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
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Exploring the inhibitory mechanisms of indazole compounds against SAH/MTAN-mediated quorum sensing utilizing QSAR and docking. Drug Target Insights 2022; 16:54-68. [PMID: 36582781 PMCID: PMC9788832 DOI: 10.33393/dti.2022.2512] [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: 10/26/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The world is under the great threat of antimicrobial resistance (AMR) leading to premature deaths. Microorganisms can produce AMR via quorum sensing mechanisms utilizing S-adenosyl homocysteine/methylthioadenosine nucleosidase (SAH/MTAN) biosynthesis. But there is no specific drug developed to date to stop SAH/MTAN, which is a crucial target for the discovery of anti-quorum sensing compound. It has been shown that indazole compounds cause inhibition of SAH/MTAN-mediated quorum sensing, but the biochemical mechanisms have not yet been explored. Therefore, in this original research, an attempt has been made to explore essential structural features of these compounds by quantitative structure-activity relationship (QSAR) and molecular docking of indazole compounds having inhibition of SAH/MTAN-mediated quorum sensing. The validated QSAR predicted five essential descriptors and molecular docking helps to identify the active binding amino acid residues involved in ligand-receptor interactions that are responsible for producing the quorum sensing inhibitory mechanisms of indazole compounds against SAH/MTAN-mediated AMR.
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25
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Ma Y, Yan J, Yang L, Yao Y, Wang L, Gao SS, Cui C. A hybrid system for the overproduction of complex ergot alkaloid chanoclavine. Front Bioeng Biotechnol 2022; 10:1095464. [PMID: 36619381 PMCID: PMC9811125 DOI: 10.3389/fbioe.2022.1095464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Synthetic biology-based methods (Sbio) and chemical synthesis (Csyn) are two independent approaches that are both widely used for synthesizing biomolecules. In the current study, two systems were combined for the overproduction of chanoclavine (CC), a structurally complex ergot alkaloid. The whole synthetic pathway for CC was split into three sections: enzymatic synthesis of 4-Br-Trp (4-Bromo-trptophan) using cell-lysate catalysis (CLC), chemical synthesis of prechanoclavine (PCC) from 4-Br-Trp, and overproduction CC from PCC using a whole-cell catalysis (WCC) platform. The final titer of the CC is over 3 g/L in this Sbio-Csyn hybrid system, the highest yield reported so far, to the best of our knowledge. The development of such a combined route could potentially avoid the limitations of both Sbio and Csyn systems and boost the overproduction of complex natural products.
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Affiliation(s)
- Yaqing Ma
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,University of Chinese Academy of Sciences, Beijing, China
| | - Juzhang Yan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Lujia Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yongpeng Yao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Luoyi Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,*Correspondence: Luoyi Wang, ; Shu-Shan Gao, ; Chengsen Cui,
| | - Shu-Shan Gao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China,*Correspondence: Luoyi Wang, ; Shu-Shan Gao, ; Chengsen Cui,
| | - Chengsen Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China,National Technology Innovation Center of Synthetic Biology, Tianjin, China,*Correspondence: Luoyi Wang, ; Shu-Shan Gao, ; Chengsen Cui,
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26
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Production of Bacterial Cellulose in the Medium with Yeasts Pre-Fermented Coconut Water or with Addition of Selected Amino Acids. Foods 2022; 11:foods11223627. [PMID: 36429219 PMCID: PMC9689973 DOI: 10.3390/foods11223627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
The uncontrolled natural pre-fermentation process of coconut water represents great hidden safety hazards, unstable production, and impact on the quality of nata de coco-the trade name of bacterial cellulose (BC) in food industry. In this study, BC production from Komagataeibacter nataicola Q2 was conducted in the media of coconut water (50%, v/v) pre-fermented by 11 coconut-sourced yeast strains in static. Results suggested that coconut water pre-fermented by different yeast strains had varied effects on the production of BC. Compared with the use of fresh coconut water, the use of coconut water pre-fermented by Saccharomyces cerevisiae SC7 increased the BC yield by 165%. Both natural pre-fermentation and SC7 pre-fermentation altered the concentrations of amino acids in fresh coconut water. The addition of selected amino acids aspartic acid, glutamic acid, serine, methionine, threonine, isoleucine, phenylalanine, and proline at different concentrations had varied effects on the production of BC. The yield of BC was the highest when adding 3.0% (w/v) methionine. Moreover, adding 3.0% methionine allowed the production of BC with larger loops of looser aggregated microfibers, increased the crystallinity of BC from 64.8% to 69.4%, but decreased the temperature of maximum weight loss rate, hardness, and adhesiveness from 223 °C, 8.68 kg, and 92.8 g.sec to 212 °C, 7.01 kg, and 58.5 g.sec, respectively, in the test condition.
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27
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Sasajima Y, Kato T, Miyata T, Kawamoto A, Namba K, Miyata M. Isolation and structure of the fibril protein, a major component of the internal ribbon for Spiroplasma swimming. Front Microbiol 2022; 13:1004601. [PMID: 36274716 PMCID: PMC9582952 DOI: 10.3389/fmicb.2022.1004601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/01/2022] [Indexed: 11/05/2022] Open
Abstract
Spiroplasma, which are known pathogens and commensals of arthropods and plants, are helical-shaped bacteria that lack a peptidoglycan layer. Spiroplasma swim by alternating between left- and right-handed helicity. Of note, this system is not related to flagellar motility, which is widespread in bacteria. A helical ribbon running along the inner side of the helical cell should be responsible for cell helicity and comprises the bacterial actin homolog, MreB, and a protein specific to Spiroplasma, fibril. Here, we isolated the ribbon and its major component, fibril filament, for electron microscopy (EM) analysis. Single-particle analysis of the fibril filaments using the negative-staining EM revealed a three-dimensional chain structure composed of rings with a size of 11 nm wide and 6 nm long, connected by a backbone cylinder with an 8.7 nm interval with a twist along the filament axis. This structure was verified through EM tomography of quick-freeze deep-etch replica sample, with a focus on its handedness. The handedness and pitch of the helix for the isolated ribbon and fibril filament agreed with those of the cell in the resting state. Structures corresponding to the alternative state were not identified. These results suggest that the helical cell structure is supported by fibril filaments; however, the helical switch is caused by the force generated by the MreB proteins. The isolation and structural outline of the fibril filaments provide crucial information for an in-depth clarification of the unique swimming mechanism of Spiroplasma.
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Affiliation(s)
- Yuya Sasajima
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan,RIKEN Center for Biosystems Dynamics Research and Spring-8 Center, Suita, Osaka, Japan,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka Metropolitan University, Osaka, Japan,*Correspondence: Makoto Miyata,
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28
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Microbial co-occurrence network in the rhizosphere microbiome: its association with physicochemical properties and soybean yield at a regional scale. J Microbiol 2022; 60:986-997. [DOI: 10.1007/s12275-022-2363-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 10/14/2022]
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29
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Helmy YA, Kathayat D, Deblais L, Srivastava V, Closs G, Tokarski RJ, Ayinde O, Fuchs JR, Rajashekara G. Evaluation of Novel Quorum Sensing Inhibitors Targeting Auto-Inducer 2 (AI-2) for the Control of Avian Pathogenic Escherichia coli Infections in Chickens. Microbiol Spectr 2022; 10:e0028622. [PMID: 35583333 PMCID: PMC9241644 DOI: 10.1128/spectrum.00286-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/18/2022] [Indexed: 12/16/2022] Open
Abstract
Avian pathogenic Escherichia coli (APEC) associated with colibacillosis results in high morbidity and mortality, and severe economic losses to the poultry industry. APEC is a zoonotic pathogen and can infect humans through contaminated poultry products. Vaccination and antibiotic treatment are currently used to control APEC infections; however, the limited effect of vaccines and the emergence of antibiotic-resistant strains have necessitated the development of novel therapeutics. Here, we evaluated seven quorum sensing inhibitors (QSI) identified in our previous study, in APEC-infected chickens. QSIs were administered orally (~92 to 120 μg/bird) and chickens were challenged subcutaneously with APEC. Among them, QSI-5 conferred the best protection (100% reduction in mortality, 82% to 93% reduction in lesions [airsacculitis, perihepatitis, lung congestion, pericarditis] severity, and 5.2 to 6.1 logs reduction in APEC load). QSI-5 was further tested in chickens raised on built-up floor litter using an optimized dose (1 mg/L) in drinking water. QSI-5 reduced the mortality (88.4%), lesion severity (72.2%), and APEC load (2.8 logs) in chickens, which was better than the reduction observed with currently used antibiotic sulfadimethoxine (SDM; mortality 35.9%; lesion severity up to 36.9%; and APEC load up to 2.4 logs). QSI-5 was detected in chicken's blood after 0.5 h with no residues in muscle, liver, and kidney. QSI-5 increased the body weight gain with no effect on the feed conversion ratio and cecal microbiota of the chickens. Metabolomic studies revealed reduced levels of 5'-methylthioadenosine in QSI-5-treated chicken serum. In conclusion, QSI-5 displayed promising effects in chickens and thus, represents a novel anti-APEC therapeutic. IMPORTANCE Avian pathogenic Escherichia coli (APEC), a subgroup of ExPEC, is a zoonotic pathogen with public health importance. Quorum sensing is a mechanism that regulates virulence, biofilm formation, and pathogenesis in bacteria. Here, we identified a novel quorum sensing autoinducer-2 inhibitor, QSI-5, which showed higher anti-APEC efficacy in chickens compared to the currently used antibiotic, sulfadimethoxine at a much lower dose (up to 4,500 times). QSI-5 is readily absorbed with no residues in the tissues. QSI-5 also increased the chicken's body weight gain and did not impact the cecal microbiota composition. Overall, QSI-5 represents a promising lead compound for developing novel anti-virulence therapies with significant implications for treating APEC infections in chickens as well as other ExPEC associated infections in humans. Further identification of its target(s) and understanding the mechanism of action of QSI-5 in APEC will add to the future novel drug development efforts that can overcome the antimicrobial resistance problem.
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Affiliation(s)
- Yosra A. Helmy
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, Ohio, USA
| | - Dipak Kathayat
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, Ohio, USA
| | - Loic Deblais
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, Ohio, USA
| | - Vishal Srivastava
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, Ohio, USA
| | - Gary Closs
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, Ohio, USA
| | - Robert J. Tokarski
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Oluwatosin Ayinde
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - James R. Fuchs
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Gireesh Rajashekara
- Center for Food Animal Health, Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, Ohio, USA
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30
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Abdelraheem E, Thair B, Varela RF, Jockmann E, Popadić D, Hailes HC, Ward JM, Iribarren AM, Lewkowicz ES, Andexer JN, Hagedoorn PL, Hanefeld U. Methyltransferases, functions and applications. Chembiochem 2022; 23:e202200212. [PMID: 35691829 PMCID: PMC9539859 DOI: 10.1002/cbic.202200212] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/10/2022] [Indexed: 11/25/2022]
Abstract
In this review the current state‐of‐the‐art of S‐adenosylmethionine (SAM)‐dependent methyltransferases and SAM are evaluated. Their structural classification and diversity is introduced and key mechanistic aspects presented which are then detailed further. Then, catalytic SAM as a target for drugs, and approaches to utilise SAM as a cofactor in synthesis are introduced with different supply and regeneration approaches evaluated. The use of SAM analogues are also described. Finally O‐, N‐, C‐ and S‐MTs, their synthetic applications and potential for compound diversification is given.
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Affiliation(s)
| | - Benjamin Thair
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - Romina Fernández Varela
- Universidad nacional di Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Emely Jockmann
- Albert-Ludwigs-Universitat Freiburg Universitatsbibliothek Freiburg, Pharmacie, GERMANY
| | | | - Helen C Hailes
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - John M Ward
- University College London, Department of Biochemical Engineering, UNITED KINGDOM
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | | | | | - Ulf Hanefeld
- Technische Universiteit Delft, Gebouw voor Scheikunde, Julianalaan 136, 2628 BL, Delft, NETHERLANDS
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31
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Rudenko AY, Mariasina SS, Sergiev PV, Polshakov VI. Analogs of S-Adenosyl-L-Methionine in Studies of Methyltransferases. Mol Biol 2022; 56:229-250. [PMID: 35440827 PMCID: PMC9009987 DOI: 10.1134/s002689332202011x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 01/02/2023]
Abstract
Methyltransferases (MTases) play an important role in the functioning of living systems, catalyzing the methylation reactions of DNA, RNA, proteins, and small molecules, including endogenous compounds and drugs. Many human diseases are associated with disturbances in the functioning of these enzymes; therefore, the study of MTases is an urgent and important task. Most MTases use the cofactor S‑adenosyl‑L‑methionine (SAM) as a methyl group donor. SAM analogs are widely applicable in the study of MTases: they are used in studies of the catalytic activity of these enzymes, in identification of substrates of new MTases, and for modification of the substrates or substrate linking to MTases. In this review, new synthetic analogs of SAM and the problems that can be solved with their usage are discussed.
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Affiliation(s)
- A. Yu. Rudenko
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Zelinsky Institute of Organic Chemistry, 119991 Moscow, Russia
| | - S. S. Mariasina
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - P. V. Sergiev
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - V. I. Polshakov
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
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32
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Degano M. Structure, Oligomerization and Activity Modulation in N-Ribohydrolases. Int J Mol Sci 2022; 23:ijms23052576. [PMID: 35269719 PMCID: PMC8910321 DOI: 10.3390/ijms23052576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Enzymes catalyzing the hydrolysis of the N-glycosidic bond in nucleosides and other ribosides (N-ribohydrolases, NHs) with diverse substrate specificities are found in all kingdoms of life. While the overall NH fold is highly conserved, limited substitutions and insertions can account for differences in substrate selection, catalytic efficiency, and distinct structural features. The NH structural module is also employed in monomeric proteins devoid of enzymatic activity with different physiological roles. The homo-oligomeric quaternary structure of active NHs parallels the different catalytic strategies used by each isozyme, while providing a buttressing effect to maintain the active site geometry and allow the conformational changes required for catalysis. The unique features of the NH catalytic strategy and structure make these proteins attractive targets for diverse therapeutic goals in different diseases.
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Affiliation(s)
- Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS Scientific Institute San Raffaele, via Olgettina 60, 20132 Milano, Italy;
- Università Vita-Salute San Raffaele, via Olgettina 58, 20132 Milano, Italy
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33
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Liu Q, Lin B, Tao Y. Improved methylation in E. coli via an efficient methyl supply system driven by betaine. Metab Eng 2022; 72:46-55. [DOI: 10.1016/j.ymben.2022.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 12/21/2022]
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34
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Shahrear S, Afroj Zinnia M, Sany MRU, Islam ABMMK. Functional Analysis of Hypothetical Proteins of Vibrio parahaemolyticus Reveals the Presence of Virulence Factors and Growth-Related Enzymes With Therapeutic Potential. Bioinform Biol Insights 2022; 16:11779322221136002. [PMID: 36386863 PMCID: PMC9661560 DOI: 10.1177/11779322221136002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/30/2022] [Indexed: 11/11/2022] Open
Abstract
Vibrio parahaemolyticus, an aquatic pathogen, is a major concern in the shrimp aquaculture industry. Several strains of this pathogen are responsible for causing acute hepatopancreatic necrosis disease as well as other serious illness, both of which result in severe economic losses. The genome sequence of two pathogenic strains of V. parahaemolyticus, MSR16 and MSR17, isolated from Bangladesh, have been reported to gain a better understanding of their diversity and virulence. However, the prevalence of hypothetical proteins (HPs) makes it challenging to obtain a comprehensive understanding of the pathogenesis of V. parahaemolyticus. The aim of the present study is to provide a functional annotation of the HPs to elucidate their role in pathogenesis employing several in silico tools. The exploration of protein domains and families, similarity searches against proteins with known function, gene ontology enrichment, along with protein-protein interaction analysis of the HPs led to the functional assignment with a high level of confidence for 656 proteins out of a pool of 2631 proteins. The in silico approach used in this study was important for accurately assigning function to HPs and inferring interactions with proteins with previously described functions. The HPs with function predicted were categorized into various groups such as enzymes involved in small-compound biosynthesis pathway, iron binding proteins, antibiotics resistance proteins, and other proteins. Several proteins with potential druggability were identified among them. In addition, the HPs were investigated in search of virulent factors, which led to the identification of proteins that have the potential to be exploited as vaccine candidate. The findings of the study will be effective in gaining a better understanding of the molecular mechanisms of bacterial pathogenesis. They may also provide an insight into the process of evaluating promising targets for the development of drugs and vaccines against V. parahaemolyticus.
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Affiliation(s)
- Sazzad Shahrear
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | | | - Md. Rabi Us Sany
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
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Liu H, Zhu J, Li Q, Wang D, Wan K, Yuan Z, Zhang J, Zou L, He X, Miao J. Untargeted metabolomic analysis of urine samples for diagnosis of inherited metabolic disorders. Funct Integr Genomics 2021; 21:645-653. [PMID: 34585279 DOI: 10.1007/s10142-021-00804-w] [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: 04/21/2021] [Revised: 08/07/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022]
Abstract
Metabolomics has become an important tool for clinical research, especially for analyzing inherited metabolic disorders (IMDs). The purpose of this study was to explore the performance of metabolomics in diagnosing IMDs using an untargeted metabolomic approach. A total of 40 urine samples were collected: 20 samples from healthy children and 20 from pediatric patients, of whom 13 had confirmed IMDs and seven had suspected IMDs. Samples were analyzed by Orbitrap mass spectrometry in positive and negative mode alternately, coupled with ultra-high liquid chromatography. Raw data were processed using Compound Discovery 2.0 ™ and then exported for partial least squares discriminant analysis (PLS-DA) by SIMCA-P 14.1. After comparing with m/zCloud and chemSpider libraries, compounds with similarity above 80% were selected and normalized for subsequent relative quantification analysis. The uncommon compounds discovered were analyzed based on the Kyoto Encyclopedia of Genes and Genomes to explore their possible metabolic pathways. All IMDs patients were successfully distinguished from controls in the PLS-DA. Untargeted metabolomics revealed a broader metabolic spectrum in patients than what is observed using routine chromatographic methods for detecting IMDs. Higher levels of certain compounds were found in all 13 confirmed IMD patients and 5 of 7 suspected IMD patients. Several potential novel markers emerged after relative quantification. Untargeted metabolomics may be able to diagnose IMDs from urine and may deepen insights into the disease by revealing changes in various compounds such as amino acids, acylcarnitines, organic acids, and nucleosides. Such analyses may identify biomarkers to improve the study and treatment of IMDs.
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Affiliation(s)
- Hao Liu
- Newborn Screening Center, Chongqing Health Center for Women and Children, Longshan Road 120th, Yubei District, Chongqing, 401147, People's Republic of China.,Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Jiang Zhu
- Chongqing Key Laboratory of Child Nutrition and Health, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Qiu Li
- Chongqing Key Laboratory of Child Nutrition and Health, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Dongjuan Wang
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Kexing Wan
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Zhaojian Yuan
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Juan Zhang
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Lin Zou
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Xiaoyan He
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China.
| | - Jingkun Miao
- Newborn Screening Center, Chongqing Health Center for Women and Children, Longshan Road 120th, Yubei District, Chongqing, 401147, People's Republic of China.
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Sasajima Y, Miyata M. Prospects for the Mechanism of Spiroplasma Swimming. Front Microbiol 2021; 12:706426. [PMID: 34512583 PMCID: PMC8432965 DOI: 10.3389/fmicb.2021.706426] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/12/2021] [Indexed: 11/18/2022] Open
Abstract
Spiroplasma are helical bacteria that lack a peptidoglycan layer. They are widespread globally as parasites of arthropods and plants. Their infectious processes and survival are most likely supported by their unique swimming system, which is unrelated to well-known bacterial motility systems such as flagella and pili. Spiroplasma swims by switching the left- and right-handed helical cell body alternately from the cell front. The kinks generated by the helicity shift travel down along the cell axis and rotate the cell body posterior to the kink position like a screw, pushing the water backward and propelling the cell body forward. An internal structure called the "ribbon" has been focused to elucidate the mechanisms for the cell helicity formation and swimming. The ribbon is composed of Spiroplasma-specific fibril protein and a bacterial actin, MreB. Here, we propose a model for helicity-switching swimming focusing on the ribbon, in which MreBs generate a force like a bimetallic strip based on ATP energy and switch the handedness of helical fibril filaments. Cooperative changes of these filaments cause helicity to shift down the cell axis. Interestingly, unlike other motility systems, the fibril protein and Spiroplasma MreBs can be traced back to their ancestors. The fibril protein has evolved from methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase, which is essential for growth, and MreBs, which function as a scaffold for peptidoglycan synthesis in walled bacteria.
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Affiliation(s)
- Yuya Sasajima
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
- The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
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Zhang C, Sultan SA, T R, Chen X. Biotechnological applications of S-adenosyl-methionine-dependent methyltransferases for natural products biosynthesis and diversification. BIORESOUR BIOPROCESS 2021; 8:72. [PMID: 38650197 PMCID: PMC10992897 DOI: 10.1186/s40643-021-00425-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/31/2021] [Indexed: 12/28/2022] Open
Abstract
In the biosynthesis of natural products, methylation is a common and essential transformation to alter molecules' bioavailability and bioactivity. The main methylation reaction is performed by S-adenosylmethionine (SAM)-dependent methyltransferases (MTs). With advancements in genomic and chemical profiling technologies, novel MTs have been discovered to accept complex substrates and synthesize industrially valuable natural products. However, to achieve a high yield of small molecules in microbial hosts, many methyltransferase activities have been reported to be insufficient. Moreover, inadequate co-factor supplies and feedback inhibition of the by-product, S-adenosylhomocysteine (SAH), further limit MTs' activities. Here, we review recent advances in SAM-dependent MTs to produce and diversify natural products. First, we surveyed recently identified novel methyltransferases in natural product biosynthesis. Second, we summarized enzyme engineering strategies to improve methyltransferase activity, with a particular focus on high-throughput assay design and application. Finally, we reviewed innovations in co-factor regeneration and diversification, both in vitro and in vivo. Noteworthily, many MTs are able to accept multiple structurally similar substrates. Such promiscuous methyltransferases are versatile and can be tailored to design de novo pathways to produce molecules whose biosynthetic pathway is unknown or non-existent in nature, thus broadening the scope of biosynthesized functional molecules.
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Affiliation(s)
- Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Stella Amelia Sultan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Rehka T
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Xixian Chen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore.
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Melo RT, Galvão NN, Guidotti-Takeuchi M, Peres PABM, Fonseca BB, Profeta R, Azevedo VAC, Monteiro GP, Brenig B, Rossi DA. Molecular Characterization and Survive Abilities of Salmonella Heidelberg Strains of Poultry Origin in Brazil. Front Microbiol 2021; 12:674147. [PMID: 34220757 PMCID: PMC8253257 DOI: 10.3389/fmicb.2021.674147] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/12/2021] [Indexed: 12/02/2022] Open
Abstract
The aim of the study was to evaluate the genotypic and phenotypic characteristics of 20 strains of S. Heidelberg (SH) isolated from broilers produced in southern Brazil. The similarity and presence of genetic determinants linked to virulence, antimicrobial resistance, biofilm formation, and in silico-predicted metabolic interactions revealed this serovar as a threat to public health. The presence of the ompC, invA, sodC, avrA, lpfA, and agfA genes was detected in 100% of the strains and the luxS gene in 70% of them. None of the strains carries the blaSHV, mcr-1, qnrA, qnrB, and qnrS genes. All strains showed a multidrug-resistant profile to at least three non-β-lactam drugs, which include colistin, sulfamethoxazole, and tetracycline. Resistance to penicillin, ceftriaxone (90%), meropenem (25%), and cefoxitin (25%) were associated with the presence of blaCTX–M and blaCMY–2 genes. Biofilm formation reached a mature stage at 25 and 37°C, especially with chicken juice (CJ) addition. The sodium hypochlorite 1% was the least efficient in controlling the sessile cells. Genomic analysis of two strains identified more than 100 virulence genes and the presence of resistance to 24 classes of antibiotics correlated to phenotypic tests. Protein-protein interaction (PPI) prediction shows two metabolic pathways correlation with biofilm formation. Virulence, resistance, and biofilm determinants must be constant monitoring in SH, due to the possibility of occurring infections extremely difficult to cure and due risk of the maintenance of the bacterium in production environments.
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Affiliation(s)
- Roberta T Melo
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Newton N Galvão
- Ministry of Agriculture, Livestock and Supply, Rio de Janeiro, Brazil
| | | | - Phelipe A B M Peres
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Belchiolina B Fonseca
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Rodrigo Profeta
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme P Monteiro
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Daise A Rossi
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
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Rapp J, Forchhammer K. 5-Deoxyadenosine Metabolism: More than "Waste Disposal". Microb Physiol 2021; 31:248-259. [PMID: 34126623 DOI: 10.1159/000516105] [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: 01/08/2021] [Accepted: 03/19/2021] [Indexed: 11/19/2022]
Abstract
5-Deoxyadenosine (5dAdo) is a by-product of many radical SAM enzyme reactions in all domains of life, and an inhibitor of the radical SAM enzymes themselves. Hence, pathways to recycle or dispose of this toxic by-product must exist but remain largely unexplored. In this review, we discuss the current knowledge about canonical and atypical 5dAdo salvage pathways that have been characterized in the last years. We highlight studies that report on how, in certain organisms, the salvage of 5dAdo via specific pathways can confer a growth advantage by providing either intermediates for the synthesis of secondary metabolites or a carbon source for the synthesis of metabolites of the central carbon metabolism. Yet, an alternative recycling route exists in organisms that use 5dAdo as a substrate to synthesize and excrete 7-deoxysedoheptulose, an allelopathic inhibitor of one enzyme of the shikimate pathway, thereby competing for their own niche. Remarkably, most steps of 5dAdo salvage are the result of the activity of promiscuous enzymes. This strategy enables even organisms with a small genome to synthesize bioactive compounds which they can deploy under certain conditions to gain a competitive growth advantage. We conclude emphasizing that, unexpectedly, 5dAdo salvage pathways seem not to be ubiquitously present, raising questions about the fate of such a toxic by-product in those species. This observation also suggests that additional 5dAdo salvage pathways, possibly relying on the activity of promiscuous enzymes, may exist. The future challenge will be to bring to light these "cryptic" 5dAdo recycling pathways.
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Affiliation(s)
- Johanna Rapp
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany
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Feng M, Harijan RK, Harris LD, Tyler PC, Fröhlich RFG, Brown M, Schramm VL. Aminofutalosine Deaminase in the Menaquinone Pathway of Helicobacter pylori. Biochemistry 2021; 60:1933-1946. [PMID: 34077175 DOI: 10.1021/acs.biochem.1c00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Helicobacter pylori is a Gram-negative bacterium that is responsible for gastric and duodenal ulcers. H. pylori uses the unusual mqn pathway with aminofutalosine (AFL) as an intermediate for menaquinone biosynthesis. Previous reports indicate that hydrolysis of AFL by 5'-methylthioadenosine nucleosidase (HpMTAN) is the direct path for producing downstream metabolites in the mqn pathway. However, genomic analysis indicates jhp0252 is a candidate for encoding AFL deaminase (AFLDA), an activity for deaminating aminofutolasine. The product, futalosine, is not a known substrate for bacterial MTANs. Recombinant jhp0252 was expressed and characterized as an AFL deaminase (HpAFLDA). Its catalytic specificity includes AFL, 5'-methylthioadenosine, 5'-deoxyadenosine, adenosine, and S-adenosylhomocysteine. The kcat/Km value for AFL is 6.8 × 104 M-1 s-1, 26-fold greater than that for adenosine. 5'-Methylthiocoformycin (MTCF) is a slow-onset inhibitor for HpAFLDA and demonstrated inhibitory effects on H. pylori growth. Supplementation with futalosine partially restored H. pylori growth under MTCF treatment, suggesting AFL deamination is significant for cell growth. The crystal structures of apo-HpAFLDA and with MTCF at the catalytic sites show a catalytic site Zn2+ or Fe2+ as the water-activating group. With bound MTCF, the metal ion is 2.0 Å from the sp3 hydroxyl group of the transition state analogue. Metabolomics analysis revealed that HpAFLDA has intracellular activity and is inhibited by MTCF. The mqn pathway in H. pylori bifurcates at aminofutalosine with HpMTAN producing adenine and depurinated futalosine and HpAFLDA producing futalosine. Inhibition of cellular HpMTAN or HpAFLDA decreased the cellular content of menaquinone-6, supporting roles for both enzymes in the pathway.
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Affiliation(s)
- Mu Feng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Rajesh K Harijan
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Lawrence D Harris
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Peter C Tyler
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Richard F G Fröhlich
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Morais Brown
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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12/111phiA Prophage Domestication Is Associated with Autoaggregation and Increased Ability to Produce Biofilm in Streptococcus agalactiae. Microorganisms 2021; 9:microorganisms9061112. [PMID: 34063935 PMCID: PMC8223999 DOI: 10.3390/microorganisms9061112] [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: 04/10/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 01/11/2023] Open
Abstract
CC17 Streptococcus agalactiae carrying group-A prophages is increasingly responsible for neonatal infections. To investigate the impact of the genetic features of a group-A prophage, we first conducted an in silico analysis of the genome of 12/111phiA, a group-A prophage carried by a strain responsible for a bloodstream infection in a parturient. This revealed a Restriction Modification system, suggesting a prophage maintenance strategy and five ORFs of interest for the host and encoding a type II toxin antitoxin system RelB/YafQ, an endonuclease, an S-adenosylmethionine synthetase MetK, and an StrP-like adhesin. Using the WT strain cured from 12/111phiA and constructing deleted mutants for the ORFs of interest, and their complemented mutants, we demonstrated an impact of prophage features on growth characteristics, cell morphology and biofilm formation. Our findings argue in favor of 12/111phiA domestication by the host and a role of prophage features in cell autoaggregation, glycocalyx and biofilm formation. We suggest that lysogeny may promote GBS adaptation to the acid environment of the vagina, consequently colonizing and infecting neonates.
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Unravelling the Molecular Mechanisms Underlying the Protective Effect of Lactate on the High-Pressure Resistance of Listeria monocytogenes. Biomolecules 2021; 11:biom11050677. [PMID: 33946460 PMCID: PMC8147161 DOI: 10.3390/biom11050677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/16/2021] [Accepted: 04/27/2021] [Indexed: 12/22/2022] Open
Abstract
Formulations with lactate as an antimicrobial and high-pressure processing (HPP) as a lethal treatment are combined strategies used to control L. monocytogenes in cooked meat products. Previous studies have shown that when HPP is applied in products with lactate, the inactivation of L. monocytogenes is lower than that without lactate. The purpose of the present work was to identify the molecular mechanisms underlying the piezo-protection effect of lactate. Two L. monocytogenes strains (CTC1034 and EGDe) were independently inoculated in a cooked ham model medium without and with 2.8% potassium lactate. Samples were pressurized at 400 MPa for 10 min at 10 °C. Samples were subjected to RNA extraction, and a shotgun transcriptome sequencing was performed. The short exposure of L. monocytogenes cells to lactate through its inoculation in a cooked ham model with lactate 1h before HPP promoted a shift in the pathogen’s central metabolism, favoring the metabolism of propanediol and ethanolamine together with the synthesis of the B12 cofactor. Moreover, the results suggest an activated methyl cycle that would promote modifications in membrane properties resulting in an enhanced resistance of the pathogen to HPP. This study provides insights on the mechanisms developed by L. monocytogenes in response to lactate and/or HPP and sheds light on the understanding of the piezo-protective effect of lactate.
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Yuan K, Hou L, Jin Q, Niu C, Mao M, Wang R, Huang Z. Comparative transcriptomics analysis of Streptococcus mutans with disruption of LuxS/AI-2 quorum sensing and recovery of methyl cycle. Arch Oral Biol 2021; 127:105137. [PMID: 33965851 DOI: 10.1016/j.archoralbio.2021.105137] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 11/16/2022]
Abstract
OBJECTIVE The LuxS/AI-2 quorum sensing (QS) system has critical roles in Streptococcus mutans cariogenicity. Whereas the molecular and cellular mechanisms of the LuxS/AI-2 QS system are not thoroughly understood. Given that LuxS has roles in QS and methyl cycle, its mutation can cause QS deficiency and methyl cycle disruption. The aim of this study was to investigate effects of the LuxS/AI-2 QS system on gene expression in Streptococcus mutans when methyl cycle was recovered with exogenous sahH gene. METHODS Our previous study introduced the exogenous sahH gene from Pseudomonas aeruginosa into an S. mutans luxS-null strain to restore the disrupted methyl cycle, and this produced the solely the LuxS/AI-2 QS system deficient strain. Here, we analyzed the transcriptomics of this strain to get insights into the molecular mechanisms of the LuxS/AI-2 QS system applying RNA-seq. RESULTS With recovery of methyl cycle, 84 genes didn't change in expression trends in S. mutans luxS-null strain. These genes mainly encode the ABC transporters, sugar transporter EII and enzymes of carbohydrate metabolism, and are rich in the Phosphotransferase system, Fructose and mannose metabolism, Amino sugar and nucleotide sugar metabolism, Galactose metabolism, Glycolysis/Gluconeogenesis, RNA degradation, Lysine biosynthesis, and Glycine, serine and threonine metabolism. CONCLUSIONS The LuxS/AI-2 QS system may mainly affect ABC transporters and carbohydrate transport, transformation and metabolism via EII subunits and enzymes to influence virulence-associated traits without effects of methyl cycle inStreptococcus mutans.
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Affiliation(s)
- Keyong Yuan
- Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai JiaoTong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Lili Hou
- Department of Nursing, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Qiaoqiao Jin
- Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai JiaoTong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Chenguang Niu
- Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai JiaoTong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Mengying Mao
- Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai JiaoTong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Ruirui Wang
- Department of Stomatology, Minhang Branch, Zhongshan Hospital, Fudan University, China.
| | - Zhengwei Huang
- Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai JiaoTong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China.
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Travin DY, Severinov K, Dubiley S. Natural Trojan horse inhibitors of aminoacyl-tRNA synthetases. RSC Chem Biol 2021; 2:468-485. [PMID: 34382000 PMCID: PMC8323819 DOI: 10.1039/d0cb00208a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/10/2021] [Indexed: 12/18/2022] Open
Abstract
For most antimicrobial compounds with intracellular targets, getting inside the cell is the major obstacle limiting their activity. To pass this barrier some antibiotics mimic the compounds of specific interest for the microbe (siderophores, peptides, carbohydrates, etc.) and hijack the transport systems involved in their active uptake followed by the release of a toxic warhead inside the cell. In this review, we summarize the information about the structures, biosynthesis, and transport of natural inhibitors of aminoacyl-tRNA synthetases (albomycin, microcin C-related compounds, and agrocin 84) that rely on such "Trojan horse" strategy to enter the cell. In addition, we provide new data on the composition and distribution of biosynthetic gene clusters reminiscent of those coding for known Trojan horse aminoacyl-tRNA synthetases inhibitors. The products of these clusters are likely new antimicrobials that warrant further investigation.
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Affiliation(s)
- Dmitrii Y Travin
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
- Waksman Institute for Microbiology, Rutgers, Piscataway New Jersey USA
| | - Svetlana Dubiley
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
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Identification of immucillin analogue natural compounds to inhibit Helicobacter pylori MTAN through high throughput virtual screening and molecular dynamics simulation. In Silico Pharmacol 2021; 9:22. [PMID: 33786292 DOI: 10.1007/s40203-021-00081-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 02/10/2021] [Indexed: 01/29/2023] Open
Abstract
Abstract One in every two humans is having Helicobacter pylori (H. pylori) in stomach causing gastric ulcer. Emergence of several drugs in eliminating H. pylori has paved way for emergence of multidrug resistance in them. This resistance is thriving and thereby necessitating the need of a potent drug. Identifying a potential target for medication is crucial. Bacterial 5'-methylthioadenosine/S-enosyl homocysteine nucleosidase (MTAN) is a multifunctional enzyme that controls seven essential metabolic pathways. It functions as a catalyst in the hydrolysis of the N-ribosidic bond of adenosine-based metabolites: S-adenosylhomocysteine (SAH), 5'-methylthioadenosine (MTA), 5'-deoxyadenosine (5'-DOA), and 6-amino-6-deoxyfutalosine. H. pylori unlike other bacteria and humans utilises an alternative pathway for menaquinone synthesis. It utilises Futosiline pathway for menaquinone synthesis which are obligatory component in electron transport pathway. Therefore, the enzymes functioning in this pathway represent them-self as a point of attack for new medications. We targeted MTAN protein of H. pylori to find out a potent natural hit to inhibit its growth. A comparative analysis was made with potent H. pylori MTAN (HpMTAN) known inhibitor, 5'-butylthio-DADMe-Immucillin-A (BuT-DADMe-ImmA) and ZINC natural subset database. Optimized ligands from the ZINC natural database were virtually screened using ligand based pharmacophore hypothesis to obtain the most efficient and potent inhibitors for HpMTAN. The screened leads were evaluated for their therapeutic likeness. Furthermore, the ligands that passed the test were subjected for MM-GBSA with MTAN to reveal the essential features that contributes selectivity. The results showed that Van der Waals contributions play a central role in determining the selectivity of MTAN. Molecular dynamics (MD) studies were carried out for 100 ns to assess the stability of ligands in the active site. MD analysis showed that binding of ZINC00490333 with MTAN is stable compared to reference inhibitor molecule BuT-DADMe-ImmA. Among the natural inhibitors screened after various docking procedures ZINC00490333 has highest binding score for HpMTAN (- 13.987). The ZINC inhibitor was successful in reproducing the BuT-DADMe-ImmA interactions with HpMTAN. Hence we suggest that ZINC00490333 compound may represent as a good lead in designing novel potent inhibitors of HpMTAN. This in silico approach indicates the potential of this molecule for advancing a further step in gastric ulcer treatment. Graphic abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00081-2.
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Mass spectrometry based targeted metabolomics precisely characterized new functional metabolites that regulate biofilm formation in Escherichia coli. Anal Chim Acta 2021; 1145:26-36. [DOI: 10.1016/j.aca.2020.12.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/17/2022]
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The critical role of MetR/ MetB/ MetC/ MetX in cysteine and methionine metabolism, fungal development and virulence of Alternaria alternata. Appl Environ Microbiol 2021; 87:AEM.01911-20. [PMID: 33277273 PMCID: PMC7851696 DOI: 10.1128/aem.01911-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Methionine is a unique sulfur-containing amino acid, which plays an important role in biological protein synthesis and various cellular processes. Here, we characterized the biological functions of AaMetB, AaMetC, and AaMetX in the tangerine pathotype of Alternaria alternata Morphological analysis showed that the mutants lacking AaMetB, AaMetC, or AaMetX resulted in less aerial hypha and fewer conidia in artificial media. Pathogenicity analysis showed that AaMetB, AaMetC, and AaMetX are required for full virulence. The defects in vegetative growth, conidiation and virulence of ΔMetB, ΔMetC, and ΔMetX can be restored by exogenous methionine and homocysteine, indicating that AaMetB, AaMetC, and AaMetX are required for methionine biosynthesis. However, exogenous cysteine only restored the growth and virulence defects of ΔMetR but not ΔMetB/C/X, suggesting that AaMetR is essential for cysteine biosynthesis. Oxidant sensitivity assay showed that only ΔMetR is sensitive to H2O2 and many ROS-generating compounds, indicating that AaMetR is essential for oxidative tolerance. Interestingly, fungicides indoor bioassays showed that only the ΔMetR mutants are susceptive to chlorothalonil, a fungicide that could bind to the cysteine of glyceraldehyde-3-phosphate dehydrogenase. Comparative transcriptome analysis showed that the inactivation of MetB, MetC, MetX, or MetR significantly affected the expression of methionine metabolism-related genes. Moreover, the inactivation of AaMetR significantly affected the expression of many genes related to glutathione metabolism, which is essential for ROS tolerance. Taken together, our study provides genetic evidence to define the critical roles of AaMetB, AaMetC, AaMetX, and AaMetR in cysteine and methionine metabolism, fungal development and virulence of Alternaria alternata IMPORTANCE The transcription factor METR regulating methionine metabolism is essential for reactive oxygen species (ROS) tolerance and virulence in many phytopathogenic fungi. However, the underlying regulatory mechanism of METR involved in this process is still unclear. In the present study, we generated AaMetB, AaMetC and AaMetX deletion mutants and compared these mutants with AaMetR disrupted mutants. Interestingly, we found that AaMetB, AaMetC and AaMetX are required for vegetative growth, conidiation, and pathogenicity in Alternaria alternata, but not for ROS tolerance and cysteine metabolism. Furthermore, we found that METR is involved in the biosynthesis of cysteine, which is an essential substrate for the biosynthesis of methionine and glutathione. This study emphasizes the critical roles of MetR, MetB, MetC, MetX in the regulation of cysteine and methionine metabolism, as well as the cross-link with glutathione-mediated ROS tolerance in phytopathogenic fungi, which provides a foundation for future investigations.
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Cardoso P, Glossop H, Meikle TG, Aburto-Medina A, Conn CE, Sarojini V, Valery C. Molecular engineering of antimicrobial peptides: microbial targets, peptide motifs and translation opportunities. Biophys Rev 2021; 13:35-69. [PMID: 33495702 PMCID: PMC7817352 DOI: 10.1007/s12551-021-00784-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
The global public health threat of antimicrobial resistance has led the scientific community to highly engage into research on alternative strategies to the traditional small molecule therapeutics. Here, we review one of the most popular alternatives amongst basic and applied research scientists, synthetic antimicrobial peptides. The ease of peptide chemical synthesis combined with emerging engineering principles and potent broad-spectrum activity, including against multidrug-resistant strains, has motivated intense scientific focus on these compounds for the past decade. This global effort has resulted in significant advances in our understanding of peptide antimicrobial activity at the molecular scale. Recent evidence of molecular targets other than the microbial lipid membrane, and efforts towards consensus antimicrobial peptide motifs, have supported the rise of molecular engineering approaches and design tools, including machine learning. Beyond molecular concepts, supramolecular chemistry has been lately added to the debate; and helped unravel the impact of peptide self-assembly on activity, including on biofilms and secondary targets, while providing new directions in pharmaceutical formulation through taking advantage of peptide self-assembled nanostructures. We argue that these basic research advances constitute a solid basis for promising industry translation of rationally designed synthetic peptide antimicrobials, not only as novel drugs against multidrug-resistant strains but also as components of emerging antimicrobial biomaterials. This perspective is supported by recent developments of innovative peptide-based and peptide-carrier nanobiomaterials that we also review.
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Affiliation(s)
- Priscila Cardoso
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia.,School of Science, RMIT University, Melbourne, Australia
| | - Hugh Glossop
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | | | | | | | - Celine Valery
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
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Xiang S, Gao M, Cao J, Shu X, Cheng M, Wang F, Deng T, Liu J. Precise identification of an RNA methyltransferase's substrate modification site. Chem Commun (Camb) 2021; 57:2499-2502. [DOI: 10.1039/d0cc08260k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A simple and nonradioactive method to probe the substrate modification site and structural preference of an RNA methyltransferase.
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Affiliation(s)
- Siying Xiang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Xiao Shu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Mohan Cheng
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Fengqin Wang
- College of Animal Sciences
- Key Laboratory of Animal Nutrition & Feed Sciences
- Ministry of Agriculture
- Zhejiang University
- Hangzhou
| | - Ting Deng
- State Key Laboratory of Genetic Engineering
- Collaborative Innovation Centre of Genetics and Development
- Department of Biochemistry
- Institute of Plant Biology
- School of Life Sciences
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
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Rapp J, Rath P, Kilian J, Brilisauer K, Grond S, Forchhammer K. A bioactive molecule made by unusual salvage of radical SAM enzyme byproduct 5-deoxyadenosine blurs the boundary of primary and secondary metabolism. J Biol Chem 2021; 296:100621. [PMID: 33811856 PMCID: PMC8102628 DOI: 10.1016/j.jbc.2021.100621] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022] Open
Abstract
5-Deoxyadenosine (5dAdo) is the byproduct of many radical S-adenosyl-l-methionine enzyme reactions in all domains of life. 5dAdo is also an inhibitor of the radical S-adenosyl-l-methionine enzymes themselves, making it necessary for cells to construct pathways to recycle or dispose of this toxic metabolite. However, the specific pathways involved have long remained unexplored. Recent research demonstrated a growth advantage in certain organisms by using 5dAdo or intermediates as a sole carbon source and elucidated the corresponding salvage pathway. We now provide evidence using supernatant analysis by GC-MS for another 5dAdo recycling route. Specifically, in the unicellular cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus), the activity of promiscuous enzymes leads to the synthesis and excretion first of 5-deoxyribose and subsequently of 7-deoxysedoheptulose. 7-Deoxysedoheptulose is an unusual deoxy-sugar, which acts as an antimetabolite of the shikimate pathway, thereby exhibiting antimicrobial and herbicidal activity. This strategy enables organisms with small genomes and lacking canonical gene clusters for the synthesis of secondary metabolites, like S. elongatus, to produce antimicrobial compounds from primary metabolism and enzymatic promiscuity. Our findings challenge the view of bioactive molecules as sole products of secondary metabolite gene clusters and expand the range of compounds that microorganisms can deploy to compete for their ecological niche.
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Affiliation(s)
- Johanna Rapp
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Pascal Rath
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Joachim Kilian
- Center for Plant Molecular Biology, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Klaus Brilisauer
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Organismic Interactions, Eberhard Karls Universität Tübingen, Tübingen, Germany.
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