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Malik A, Oludiran A, Poudel A, Alvarez OB, Woodward C, Purcell EB. RelQ-mediated alarmone signalling regulates growth, stress-induced biofilm formation and spore accumulation in Clostridioides difficile. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001479. [PMID: 39028551 PMCID: PMC11317968 DOI: 10.1099/mic.0.001479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024]
Abstract
The bacterial stringent response (SR) is a conserved transcriptional reprogramming pathway mediated by the nucleotide signalling alarmones, (pp)pGpp. The SR has been implicated in antibiotic survival in Clostridioides difficile, a biofilm- and spore-forming pathogen that causes resilient, highly recurrent C. difficile infections. The role of the SR in other processes and the effectors by which it regulates C. difficile physiology are unknown. C. difficile RelQ is a clostridial alarmone synthetase. Deletion of relQ dysregulates C. difficile growth in unstressed conditions, affects susceptibility to antibiotic and oxidative stressors and drastically reduces biofilm formation. While wild-type C. difficile displays increased biofilm formation in the presence of sublethal stress, the ΔrelQ strain cannot upregulate biofilm production in response to stress. Deletion of relQ slows spore accumulation in planktonic cultures but accelerates it in biofilms. This work establishes biofilm formation and spore accumulation as alarmone-mediated processes in C. difficile and reveals the importance of RelQ in stress-induced biofilm regulation.
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Affiliation(s)
- Areej Malik
- Biomedical Sciences Program, Old Dominion University, Norfolk, Virginia, 23529, USA
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Adenrele Oludiran
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Asia Poudel
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Orlando Berumen Alvarez
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Charles Woodward
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Erin B. Purcell
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
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Malik A, Oludiran A, Poudel A, Alvarez OB, Woodward C, Purcell EB. RelQ-mediated alarmone signaling regulates growth, sporulation, and stress-induced biofilm formation in Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580318. [PMID: 38405794 PMCID: PMC10888890 DOI: 10.1101/2024.02.14.580318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The bacterial stringent response (SR) is a conserved transcriptional reprogramming pathway mediated by the nucleotide signaling alarmones, (pp)pGpp. The SR has been implicated in antibiotic survival in Clostridioides difficile, a biofilm- and spore-forming pathogen that causes resilient, highly recurrent C. difficile infections. The role of the SR in other processes and the effectors by which it regulates C. difficile physiology are unknown. C. difficile RelQ is a clostridial alarmone synthetase. Deletion of relQ dysregulates C. difficile growth in unstressed conditions, affects susceptibility to antibiotic and oxidative stressors, and drastically reduces biofilm formation. While wild-type C. difficile displays increased biofilm formation in the presence of sub-lethal stress, the ΔrelQ strain cannot upregulate biofilm production in response to stress. Deletion of relQ slows spore accumulation in planktonic cultures but accelerates it in biofilms. This work establishes biofilm formation and sporulation as alarmone-mediated processes in C. difficile and reveals the importance of RelQ in stress-induced biofilm regulation.
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Affiliation(s)
- Areej Malik
- Biomedical Sciences Program, Old Dominion University, Norfolk, Virginia, 23529, USA
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Adenrele Oludiran
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Asia Poudel
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Orlando Berumen Alvarez
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Charles Woodward
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
| | - Erin B. Purcell
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, 23529, USA
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Kashevarova NM, Khaova EA, Tkachenko AG. The regulatory effects of (p)ppGpp and indole on cAMP synthesis in Escherichia coli cells. Vavilovskii Zhurnal Genet Selektsii 2024; 28:15-23. [PMID: 38465243 PMCID: PMC10917672 DOI: 10.18699/vjgb-24-03] [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: 07/14/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 03/12/2024] Open
Abstract
Bacterial stress adaptive response is formed due to changes in the cell gene expression profile in response to alterations in environmental conditions through the functioning of regulatory networks. The mutual influence of network signaling molecules represented by cells' natural metabolites, including indole and second messengers (p) ppGpp and cAMP, is hitherto not well understood, being the aim of this study. E. coli parent strain BW25141 ((p) ppGpp+) and deletion knockout BW25141ΔrelAΔspoT which is unable to synthesize (p)ppGpp ((p)ppGpp0) were cultivated in M9 medium supplemented with different glucose concentrations (5.6 and 22.2 mM) in the presence of tryptophan as a substrate for indole synthesis and in its absence. The glucose content was determined with the glucose oxidase method; the indole content, by means of HPLC; and the cAMP concentration, by ELISA. The onset of an increase in initially low intracellular cAMP content coincided with the depletion of glucose in the medium. Maximum cAMP accumulation in the cells was proportional to the concentration of initially added glucose. At the same time, the (p) ppGpp0 mutant showed a decrease in maximum cAMP levels compared to the (p)ppGpp+ parent, which was the most pronounced in the medium with 22.2 mM glucose. So, (p)ppGpp was able to positively regulate cAMP formation. The promoter of the tryptophanase operon responsible for indole biosynthesis is known to be under the positive control of catabolic repression. Therefore, in the cells of the (p)ppGpp+ strain grown in the tryptophan-free medium that were characterized by a low rate of spontaneous indole formation, its synthesis significantly increased in response to the rising cAMP level just after glucose depletion. However, this was not observed in the (p)ppGpp0 mutant cells with reduced cAMP accumulation. When tryptophan was added to the medium, both of these strains demonstrated high indole production, which was accompanied by a decrease in cAMP accumulation compared to the tryptophan-free control. Thus, under glucose depletion, (p)ppGpp can positively regulate the accumulation of both cAMP and indole, while the latter, in its turn, has a negative effect on cAMP formation.
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Affiliation(s)
- N M Kashevarova
- Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
| | - E A Khaova
- Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
| | - A G Tkachenko
- Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm, Russia
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Ariute JC, Coelho-Rocha ND, Dantas CWD, de Vasconcelos LAT, Profeta R, de Jesus Sousa T, de Souza Novaes A, Galotti B, Gomes LG, Gimenez EGT, Diniz C, Dias MV, de Jesus LCL, Jaiswal AK, Tiwari S, Carvalho R, Benko-Iseppon AM, Brenig B, Azevedo V, Barh D, Martins FS, Aburjaile F. Probiogenomics of Leuconostoc Mesenteroides Strains F-21 and F-22 Isolated from Human Breast Milk Reveal Beneficial Properties. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10170-7. [PMID: 37804433 DOI: 10.1007/s12602-023-10170-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 10/09/2023]
Abstract
Bacteria of the Leuconostoc genus are Gram-positive bacteria that are commonly found in raw milk and persist in fermented dairy products and plant food. Studies have already explored the probiotic potential of L. mesenteroides, but not from a probiogenomic perspective, which aims to explore the molecular features responsible for their phenotypes. In the present work, probiogenomic approaches were applied in strains F-21 and F-22 of L. mesenteroides isolated from human milk to assess their biosafety at the molecular level and to correlate molecular features with their potential probiotic characteristics. The complete genome of strain F-22 is 1.99 Mb and presents one plasmid, while the draft genome of strain F-21 is 1.89 Mb and presents four plasmids. A high percentage of average nucleotide identity among other genomes of L. mesenteroides (≥ 96%) corroborated the previous taxonomic classification of these isolates. Genomic regions that influence the probiotic properties were identified and annotated. Both strains exhibited wide genome plasticity, cell adhesion ability, proteolytic activity, proinflammatory and immunomodulation capacity through interaction with TLR-NF-κB and TLR-MAPK pathway components, and no antimicrobial resistance, denoting their potential to be candidate probiotics. Further, the strains showed bacteriocin production potential and the presence of acid, thermal, osmotic, and bile salt resistance genes, indicating their ability to survive under gastrointestinal stress. Taken together, our results suggest that L. mesenteroides F-21 and F-22 are promising candidates for probiotics in the food and pharmaceutical industries.
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Affiliation(s)
- Juan Carlos Ariute
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Nina Dias Coelho-Rocha
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Carlos Willian Dias Dantas
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Larissa Amorim Tourinho de Vasconcelos
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Rodrigo Profeta
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Thiago de Jesus Sousa
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Ane de Souza Novaes
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Bruno Galotti
- Laboratory of Biotherapeutic Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Lucas Gabriel Gomes
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Enrico Giovanelli Toccani Gimenez
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Carlos Diniz
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Mariana Vieira Dias
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Luís Cláudio Lima de Jesus
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Arun Kumar Jaiswal
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Sandeep Tiwari
- Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, 40231-300, Brazil
| | - Rodrigo Carvalho
- Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, 40231-300, Brazil
| | - Ana Maria Benko-Iseppon
- Laboratory of Plants Genetics and Biotechnology, Genetics Department, Biosciences Center, Federal University of Pernambuco, Recife, Pernambuco, 50740-600, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, 721172, India
| | - Flaviano S Martins
- Laboratory of Biotherapeutic Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Flavia Aburjaile
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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Cutugno L, O'Byrne C, Pané‐Farré J, Boyd A. Rifampicin-resistant RpoB S522L Vibrio vulnificus exhibits disturbed stress response and hypervirulence traits. Microbiologyopen 2023; 12:e1379. [PMID: 37877661 PMCID: PMC10493491 DOI: 10.1002/mbo3.1379] [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: 05/17/2023] [Revised: 08/15/2023] [Accepted: 08/31/2023] [Indexed: 10/26/2023] Open
Abstract
Rifampicin resistance, which is genetically linked to mutations in the RNA polymerase β-subunit gene rpoB, has a global impact on bacterial transcription and cell physiology. Previously, we identified a substitution of serine 522 in RpoB (i.e., RpoBS522L ) conferring rifampicin resistance to Vibrio vulnificus, a human food-borne and wound-infecting pathogen associated with a high mortality rate. Transcriptional and physiological analysis of V. vulnificus expressing RpoBS522L showed increased basal transcription of stress-related genes and global virulence regulators. Phenotypically these transcriptional changes manifest as disturbed osmo-stress responses and toxin-associated hypervirulence as shown by reduced hypoosmotic-stress resistance and enhanced cytotoxicity of the RpoBS522L strain. These results suggest that RpoB-linked rifampicin resistance has a significant impact on V. vulnificus survival in the environment and during infection.
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Affiliation(s)
- Laura Cutugno
- School of Natural SciencesUniversity of GalwayGalwayIreland
| | - Conor O'Byrne
- School of Biological and Chemical SciencesUniversity of GalwayGalwayIreland
| | - Jan Pané‐Farré
- Centre for Synthetic Microbiology (SYNMIKRO) & Department of ChemistryPhilipps‐University MarburgMarburgGermany
| | - Aoife Boyd
- School of Natural SciencesUniversity of GalwayGalwayIreland
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Protein-Ligand Interactions in Scarcity: The Stringent Response from Bacteria to Metazoa, and the Unanswered Questions. Int J Mol Sci 2023; 24:ijms24043999. [PMID: 36835415 PMCID: PMC9965611 DOI: 10.3390/ijms24043999] [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: 12/23/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
The stringent response, originally identified in Escherichia coli as a signal that leads to reprogramming of gene expression under starvation or nutrient deprivation, is now recognized as ubiquitous in all bacteria, and also as part of a broader survival strategy in diverse, other stress conditions. Much of our insight into this phenomenon derives from the role of hyperphosphorylated guanosine derivatives (pppGpp, ppGpp, pGpp; guanosine penta-, tetra- and tri-phosphate, respectively) that are synthesized on starvation cues and act as messengers or alarmones. These molecules, collectively referred to here as (p)ppGpp, orchestrate a complex network of biochemical steps that eventually lead to the repression of stable RNA synthesis, growth, and cell division, while promoting amino acid biosynthesis, survival, persistence, and virulence. In this analytical review, we summarize the mechanism of the major signaling pathways in the stringent response, consisting of the synthesis of the (p)ppGpp, their interaction with RNA polymerase, and diverse factors of macromolecular biosynthesis, leading to differential inhibition and activation of specific promoters. We also briefly touch upon the recently reported stringent-like response in a few eukaryotes, which is a very disparate mechanism involving MESH1 (Metazoan SpoT Homolog 1), a cytosolic NADPH phosphatase. Lastly, using ppGpp as an example, we speculate on possible pathways of simultaneous evolution of alarmones and their multiple targets.
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Uruén C, García C, Fraile L, Tommassen J, Arenas J. How Streptococcus suis escapes antibiotic treatments. Vet Res 2022; 53:91. [DOI: 10.1186/s13567-022-01111-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
AbstractStreptococcus suis is a zoonotic agent that causes sepsis and meningitis in pigs and humans. S. suis infections are responsible for large economic losses in pig production. The lack of effective vaccines to prevent the disease has promoted the extensive use of antibiotics worldwide. This has been followed by the emergence of resistance against different classes of antibiotics. The rates of resistance to tetracyclines, lincosamides, and macrolides are extremely high, and resistance has spread worldwide. The genetic origin of S. suis resistance is multiple and includes the production of target-modifying and antibiotic-inactivating enzymes and mutations in antibiotic targets. S. suis genomes contain traits of horizontal gene transfer. Many mobile genetic elements carry a variety of genes that confer resistance to antibiotics as well as genes for autonomous DNA transfer and, thus, S. suis can rapidly acquire multiresistance. In addition, S. suis forms microcolonies on host tissues, which are associations of microorganisms that generate tolerance to antibiotics through a variety of mechanisms and favor the exchange of genetic material. Thus, alternatives to currently used antibiotics are highly demanded. A deep understanding of the mechanisms by which S. suis becomes resistant or tolerant to antibiotics may help to develop novel molecules or combinations of antimicrobials to fight these infections. Meanwhile, phage therapy and vaccination are promising alternative strategies, which could alleviate disease pressure and, thereby, antibiotic use.
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Tan MF, Tan J, Zhang FF, Li HQ, Ji HY, Fang SP, Wu CC, Rao YL, Zeng YB, Yang Q. Exogenous glycogen utilization effects the transcriptome and pathogenicity of Streptococcus suis serotype 2. Front Cell Infect Microbiol 2022; 12:938286. [DOI: 10.3389/fcimb.2022.938286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/24/2022] [Indexed: 11/10/2022] Open
Abstract
Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen that causes severe infections in humans and the swine industry. Acquisition and utilization of available carbon sources from challenging host environments is necessary for bacterial pathogens to ensure growth and proliferation. Glycogen is abundant in mammalian body and may support the growth of SS2 during infection in hosts. However, limited information is known about the mechanism between the glycogen utilization and host adaptation of SS2. Here, the pleiotropic effects of exogenous glycogen on SS2 were investigated through transcriptome sequencing. Analysis of transcriptome data showed that the main basic metabolic pathways, especially the core carbon metabolism pathways and virulence-associated factors, of SS2 responded actively to glycogen induction. Glycogen induction led to the perturbation of the glycolysis pathway and citrate cycle, but promoted the pentose phosphate pathway and carbohydrate transport systems. Extracellular glycogen utilization also promoted the mixed-acid fermentation in SS2 rather than homolactic fermentation. Subsequently, apuA, a gene encoding the unique bifunctional amylopullulanase for glycogen degradation, was deleted from the wild type and generated the mutant strain ΔapuA. The pathogenicity details of the wild type and ΔapuA cultured in glucose and glycogen were investigated and compared. Results revealed that the capsule synthesis or bacterial morphology were not affected by glycogen incubation or apuA deletion. However, extracellular glycogen utilization significantly enhanced the hemolytic activity, adhesion and invasion ability, and lethality of SS2. The deletion of apuA also impaired the pathogenicity of bacteria cultured in glucose, indicating that ApuA is indeed an important virulence factor. Our results revealed that exogenous glycogen utilization extensively influenced the expression profile of the S. suis genome. Based on the transcriptome response, exogenous glycogen utilization promoted the carbon adaption and pathogenicity of SS2.
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Zhang T, Zhu J, Xu J, Shao H, Zhou R. Regulation of (p)ppGpp and Its Homologs on Environmental Adaptation, Survival, and Pathogenicity of Streptococci. Front Microbiol 2020; 11:1842. [PMID: 33101217 PMCID: PMC7545056 DOI: 10.3389/fmicb.2020.01842] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/14/2020] [Indexed: 11/13/2022] Open
Abstract
Most streptococci are commensals, pathogens, or opportunistic pathogens for humans and animals. Therefore, it is important for streptococci to adapt to the various challenging environments of the host during the processes of infection or colonization, as well as to in vitro conditions for transmission. Stringent response (SR) is a special class of adaptive response induced by the signal molecules (p)ppGpp, which regulate several physiological aspects, such as long-term persistence, virulence, biofilm formation, and quorum sensing in bacteria. To understand the roles of SR in streptococci, the current mini-review gives a general overview on: (1) (p)ppGpp synthetases in the genus of Streptococcus, (2) the effects of (p)ppGpp on the physiological phenotypes, persistence, and pathogenicity of streptococci, (3) the transcriptional regulation induced by (p)ppGpp in streptococci, and (4) the link between (p)ppGpp and another nutrient regulatory protein CodY in streptococci.
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Affiliation(s)
- Tengfei Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal and Veterinary Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jiawen Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Institute of Animal Sciences, Chengdu Academy of Agricultural and Forestry Sciences, Chengdu, China
| | - Jiajia Xu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huabin Shao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal and Veterinary Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,International Research Center for Animal Disease (Ministry of Science & Technology of China), Wuhan, China.,Cooperative Innovation Center of Sustainable Pig Production, Wuhan, China
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Zheng C, Wei M, Jia M, Cao M. Involvement of Various Enzymes in the Physiology and Pathogenesis of Streptococcus suis. Vet Sci 2020; 7:vetsci7040143. [PMID: 32977655 PMCID: PMC7712317 DOI: 10.3390/vetsci7040143] [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: 08/20/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022] Open
Abstract
Streptococcus suis causes severe infections in both swine and humans, making it a serious threat to the swine industry and public health. Insight into the physiology and pathogenesis of S. suis undoubtedly contributes to the control of its infection. During the infection process, a wide variety of virulence factors enable S. suis to colonize, invade, and spread in the host, thus causing localized infections and/or systemic diseases. Enzymes catalyze almost all aspects of metabolism in living organisms. Numerous enzymes have been characterized in extensive detail in S. suis, and have shown to be involved in the pathogenesis and/or physiology of this pathogen. In this review, we describe the progress in the study of some representative enzymes in S. suis, such as ATPases, immunoglobulin-degrading enzymes, and eukaryote-like serine/threonine kinase and phosphatase, and we highlight the important role of various enzymes in the physiology and pathogenesis of this pathogen. The controversies about the current understanding of certain enzymes are also discussed here. Additionally, we provide suggestions about future directions in the study of enzymes in S. suis.
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Affiliation(s)
- Chengkun Zheng
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (M.W.); (M.J.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-152-0527-9658
| | - Man Wei
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (M.W.); (M.J.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Mengdie Jia
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China; (M.W.); (M.J.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - ManMan Cao
- Guangdong Maoming Agriculture & Forestry Techical College, Maoming 525000, China;
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The (p)ppGpp Synthetase RSH Mediates Stationary-Phase Onset and Antibiotic Stress Survival in Clostridioides difficile. J Bacteriol 2020; 202:JB.00377-20. [PMID: 32661079 DOI: 10.1128/jb.00377-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 12/31/2022] Open
Abstract
The human pathogen Clostridioides difficile is increasingly tolerant of multiple antibiotics and causes infections with a high rate of recurrence, creating an urgent need for new preventative and therapeutic strategies. The stringent response, a universal bacterial response to extracellular stress, governs antibiotic survival and pathogenesis in diverse organisms but has not previously been characterized in C. difficile Here, we report that the C. difficile (p)ppGpp synthetase RSH is incapable of utilizing GTP or GMP as a substrate but readily synthesizes ppGpp from GDP. The enzyme also utilizes many structurally diverse metal cofactors for reaction catalysis and remains functionally stable at a wide range of environmental pHs. Transcription of rsh is stimulated by stationary-phase onset and by exposure to the antibiotics clindamycin and metronidazole. Chemical inhibition of RSH by the ppGpp analog relacin increases antibiotic susceptibility in epidemic C. difficile R20291, indicating that RSH inhibitors may be a viable strategy for drug development against C. difficile infection. Finally, transcriptional suppression of rsh also increases bacterial antibiotic susceptibility, suggesting that RSH contributes to C. difficile antibiotic tolerance and survival.IMPORTANCE Clostridioides difficile infection (CDI) is an urgent public health threat with a high recurrence rate, in part because the causative bacterium has a high rate of antibiotic survival. The (p)ppGpp-mediated bacterial stringent response plays a role in antibiotic tolerance in diverse pathogens and is a potential target for development of new antimicrobials because the enzymes that metabolize (p)ppGpp have no mammalian homologs. We report that stationary-phase onset and antibiotics induce expression of the clostridial ppGpp synthetase RSH and that both chemical inhibition and translational suppression of RSH increase C. difficile antibiotic susceptibility. This demonstrates that development of RSH inhibitors to serve as adjuvants to antibiotic therapy is a potential approach for the development of new strategies to combat CDI.
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Rousset L, Alpha-Bazin B, Château A, Armengaud J, Clavel T, Berge O, Duport C. Groundwater promotes emergence of asporogenic mutants of emetic Bacillus cereus. Environ Microbiol 2020; 22:5248-5264. [PMID: 32815215 DOI: 10.1111/1462-2920.15203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 01/15/2023]
Abstract
Bacillus cereus is a ubiquitous endospore-forming bacterium, which mainly affects humans as a food-borne pathogen. Bacillus cereus can contaminate groundwater used to irrigate food crops. Here, we examined the ability of the emetic strain B. cereus F4810/72 to survive abiotic conditions encountered in groundwater. Our results showed that vegetative B. cereus cells rapidly evolved in a mixed population composed of endospores and asporogenic variants bearing spo0A mutations. One asporogenic variant, VAR-F48, was isolated and characterized. VAR-F48 can survive in sterilized groundwater over a long period in a vegetative form and has a competitive advantage compared to its parental strain. Proteomics analysis allowed us to quantify changes to cellular and exoproteins after 24 and 72 h incubation in groundwater, for VAR-F48 compared to its parental strain. The results revealed a significant re-routing of the metabolism in the absence of Spo0A. We concluded that VAR-F48 maximizes its energy use to deal with oligotrophy, and the emergence of spo0A-mutated variants may contribute to the persistence of emetic B. cereus in natural oligotrophic environments.
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Affiliation(s)
- Ludivine Rousset
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France.,INRAE, Pathologie Végétale, Montfavet, F-84140, France
| | - Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France
| | - Alice Château
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, 30200, France
| | - Thierry Clavel
- Avignon Université, INRAE, UMR SQPOV, Avignon, F-84914, France
| | - Odile Berge
- INRAE, Pathologie Végétale, Montfavet, F-84140, France
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Draft genome sequence of Parvularcula flava strain NH6-79 T, revealing its role as a cellulolytic enzymes producer. Arch Microbiol 2020; 202:2591-2597. [PMID: 32607725 DOI: 10.1007/s00203-020-01967-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 01/03/2023]
Abstract
To date, the genus Parvularcula consists of 6 species and no potential application of this genus was reported. Current study presents the genome sequence of Parvularcula flava strain NH6-79 T and its cellulolytic enzyme analysis. The assembled draft genome of strain NH6-79 T consists of 9 contigs and 7 scaffolds with 3.68 Mbp in size and GC content of 59.87%. From a total of 3,465 genes predicted, 96 of them are annotated as glycoside hydrolases (GHs). Within these GHs, 20 encoded genes are related to cellulosic biomass degradation, including 12 endoglucanases (5 GH10, 4 GH5, and 3 GH51), 2 exoglucanases (GH9) and 6 β-glucosidases (GH3). In addition, highest relative enzyme activities (endoglucanase, exoglucanase, and β-glucosidase) were observed at 27th hour when the strain was cultured in the carboxymethyl cellulose/Avicel®-containing medium for 45 h. The combination of genome analysis with experimental studies indicated the ability of strain NH6-79 T to produce extracellular endoglucanase, exoglucanase, and β-glucosidase. These findings suggest the potential of Parvularcula flava strain NH6-79 T in cellulose-containing biomass degradation and that the strain could be used in cellulosic biorefining process.
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14
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Zúñiga A, Aravena P, Pulgar R, Travisany D, Ortiz-Severín J, Chávez FP, Maass A, González M, Cambiazo V. Transcriptomic Changes of Piscirickettsia salmonis During Intracellular Growth in a Salmon Macrophage-Like Cell Line. Front Cell Infect Microbiol 2020; 9:426. [PMID: 31998656 PMCID: PMC6964531 DOI: 10.3389/fcimb.2019.00426] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/29/2019] [Indexed: 12/15/2022] Open
Abstract
Piscirickettsia salmonis is the causative agent of Piscirickettsiosis, a systemic infection of salmonid fish species. P. salmonis infects and survives in its host cell, a process that correlates with the expression of virulence factors including components of the type IVB secretion system. To gain further insights into the cellular and molecular mechanism behind the adaptive response of P. salmonis during host infection, we established an in vitro model of infection using the SHK-1 cell line from Atlantic salmon head kidney. The results indicated that in comparison to uninfected SHK-1 cells, infection significantly decreased cell viability after 10 days along with a significant increment of P. salmonis genome equivalents. At that time, the intracellular bacteria were localized within a spacious cytoplasmic vacuole. By using a whole-genome microarray of P. salmonis LF-89, the transcriptome of this bacterium was examined during intracellular growth in the SHK-1 cell line and exponential growth in broth. Transcriptome analysis revealed a global shutdown of translation during P. salmonis intracellular growth and suggested an induction of the stringent response. Accordingly, key genes of the stringent response pathway were up-regulated during intracellular growth as well as at stationary phase bacteria, suggesting a role of the stringent response on bacterial virulence. Our results also reinforce the participation of the Dot/Icm type IVB secretion system during P. salmonis infection and reveals many unexplored genes with potential roles in the adaptation to intracellular growth. Finally, we proposed that intracellular P. salmonis alternates between a replicative phase and a stationary phase in which the stringent response is activated.
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Affiliation(s)
- Alejandro Zúñiga
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile.,Blue Genomics Chile, Puerto Varas, Chile
| | - Pamela Aravena
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Dante Travisany
- FONDAP Center for Genome Regulation, Santiago, Chile.,Center for Mathematical Modeling (PIA AFB17001) and Department of Mathematical Engineering, Universidad de Chile - UMI CNRS 2807, Santiago, Chile
| | - Javiera Ortiz-Severín
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile.,Laboratorio de Microbiología de Sistemas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Center for Mathematical Modeling (PIA AFB17001) and Department of Mathematical Engineering, Universidad de Chile - UMI CNRS 2807, Santiago, Chile
| | - Alejandro Maass
- FONDAP Center for Genome Regulation, Santiago, Chile.,Center for Mathematical Modeling (PIA AFB17001) and Department of Mathematical Engineering, Universidad de Chile - UMI CNRS 2807, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
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15
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Wang C, Chen W, Xia A, Zhang R, Huang Y, Yang S, Ni L, Jin F. Carbon Starvation Induces the Expression of PprB-Regulated Genes in Pseudomonas aeruginosa. Appl Environ Microbiol 2019; 85:e01705-19. [PMID: 31492668 PMCID: PMC6821963 DOI: 10.1128/aem.01705-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/02/2019] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas aeruginosa can cause severe infections in humans. This bacterium often adopts a biofilm lifestyle that is hard to treat. In several previous studies, the PprA-PprB two-component system (TCS), which controls the expression of type IVb pili, BapA adhesin, and CupE fimbriae, was shown to be involved in biofilm formation (M. Romero, H. Silistre, L. Lovelock, V. J. Wright, K.-G. Chan, et al., Nucleic Acids Res 46:6823-6840, 2018, https://doi.org/10.1093/nar/gky324; S. de Bentzmann, C. Giraud, C. S. Bernard, V. Calderon, F. Ewald F, et al., PLoS Pathog 8:e1003052, 2012, https://doi.org/10.1371/journal.ppat.1003052). However, signals or environmental conditions that can trigger the PprA-PprB TCS are still unknown, and the molecular mechanisms of PprB-mediated biofilm formation are poorly characterized. Here, we report that carbon starvation stress (CSS) can induce the expression of pprB and genes in the PprB regulon. CSS-induced pprB transcription is mediated by the stress response sigma factor RpoS rather than the two-component sensor PprA. We also observed a strong negative regulation of PprB on the transcription of itself. Further experiments showed that PprB overexpression greatly enhanced cell-cell adhesion (CCA) and cell-surface adhesion (CSA) in P. aeruginosa Specifically, under the background of PprB overexpression, both the BapA adhesin and CupE fimbriae displayed positive effects on CCA and CSA, while the type IVb pili showed an unexpected negative effect on CCA and no effect on CSA. In addition, expression of the PprB regulon genes were significantly increased in 3-day colony biofilms, indicating a possible carbon limitation state. The CSS-RpoS-PprB-Bap/Flp/CupE pathway identified in this study provides a new perspective on the process of biofilm formation in carbon-limited environments.IMPORTANCE Typically, the determination of the external signals that can trigger a regulatory system is crucial to understand the regulatory logic and inward function of that system. The PprA-PprB two-component system was reported to be involved in biofilm formation in Pseudomonas aeruginosa, but the signals triggering this system are unknown. In this study, we found that carbon starvation stress (CSS) induces transcription of pprB and genes in the PprB regulon through an RpoS-dependent pathway. Increased PprB expression leads to enhanced cell-cell adhesion (CCA) and cell-surface adhesion (CSA) in P. aeruginosa Both CCA and CSA are largely dependent on the Bap secretion system and are moderately dependent on the CupE fimbriae. Our findings suggest that PprB reinforces the structure of biofilms under carbon-limited conditions, and the Bap secretion system and CupE fimbriae are two potential targets for biofilm treatment.
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Affiliation(s)
- Congcong Wang
- Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Wenhui Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Aiguo Xia
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Rongrong Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Yajia Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Shuai Yang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Lei Ni
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Fan Jin
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
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16
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Yus E, Lloréns-Rico V, Martínez S, Gallo C, Eilers H, Blötz C, Stülke J, Lluch-Senar M, Serrano L. Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors. Cell Syst 2019; 9:143-158.e13. [PMID: 31445891 PMCID: PMC6721554 DOI: 10.1016/j.cels.2019.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/14/2019] [Accepted: 06/27/2019] [Indexed: 11/30/2022]
Abstract
Here, we determined the relative importance of different transcriptional mechanisms in the genome-reduced bacterium Mycoplasma pneumoniae, by employing an array of experimental techniques under multiple genetic and environmental perturbations. Of the 143 genes tested (21% of the bacterium’s annotated proteins), only 55% showed an altered phenotype, highlighting the robustness of biological systems. We identified nine transcription factors (TFs) and their targets, representing 43% of the genome, and 16 regulators that indirectly affect transcription. Only 20% of transcriptional regulation is mediated by canonical TFs when responding to perturbations. Using a Random Forest, we quantified the non-redundant contribution of different mechanisms such as supercoiling, metabolic control, RNA degradation, and chromosome topology to transcriptional changes. Model-predicted gene changes correlate well with experimental data in 95% of the tested perturbations, explaining up to 70% of the total variance when also considering noise. This analysis highlights the importance of considering non-TF-mediated regulation when engineering bacteria. Full comprehensive reconstruction of a bacterial gene regulatory network achieved Genome-reduced bacterium Mycoplasma pneumoniae is robust to genetic perturbations Large part of transcription regulation in bacteria is transcription-factor independent Transcription-factor-independent regulation has a smaller dynamic range
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Affiliation(s)
- Eva Yus
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain.
| | - Verónica Lloréns-Rico
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain.
| | - Sira Martínez
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Hinnerk Eilers
- Department for General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Cedric Blötz
- Department for General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Jörg Stülke
- Department for General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain.
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17
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El-Rami F, Kong X, Parikh H, Zhu B, Stone V, Kitten T, Xu P. Analysis of essential gene dynamics under antibiotic stress in Streptococcus sanguinis. MICROBIOLOGY-SGM 2019; 164:173-185. [PMID: 29393020 PMCID: PMC5882076 DOI: 10.1099/mic.0.000595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The paradoxical response of Streptococcus sanguinis to drugs prescribed for dental and clinical practices has complicated treatment guidelines and raised the need for further investigation. We conducted a high throughput study on concomitant transcriptome and proteome dynamics in a time course to assess S. sanguinis behaviour under a sub-inhibitory concentration of ampicillin. Temporal changes at the transcriptome and proteome level were monitored to cover essential genes and proteins over a physiological map of intricate pathways. Our findings revealed that translation was the functional category in S. sanguinis that was most enriched in essential proteins. Moreover, essential proteins in this category demonstrated the greatest conservation across 2774 bacterial proteomes, in comparison to other essential functional categories like cell wall biosynthesis and energy production. In comparison to non-essential proteins, essential proteins were less likely to contain ‘degradation-prone’ amino acids at their N-terminal position, suggesting a longer half-life. Despite the ampicillin-induced stress, the transcriptional up-regulation of amino acid-tRNA synthetases and proteomic elevation of amino acid biosynthesis enzymes favoured the enriched components of essential proteins revealing ‘proteomic signatures’ that can be used to bridge the genotype–phenotype gap of S. sanguinis under ampicillin stress. Furthermore, we identified a significant correlation between the levels of mRNA and protein for essential genes and detected essential protein-enriched pathways differentially regulated through a persistent stress response pattern at late time points. We propose that the current findings will help characterize a bacterial model to study the dynamics of essential genes and proteins under clinically relevant stress conditions.
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Affiliation(s)
- Fadi El-Rami
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Xiangzhen Kong
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, VA, USA
| | - Hardik Parikh
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Bin Zhu
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, VA, USA
| | - Victoria Stone
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, VA, USA
| | - Todd Kitten
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Ping Xu
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA.,Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, VA, USA
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18
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Co-regulation of CodY and (p)ppGpp synthetases on morphology and pathogenesis of Streptococcus suis. Microbiol Res 2019; 223-225:88-98. [PMID: 31178056 DOI: 10.1016/j.micres.2019.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/28/2019] [Accepted: 04/06/2019] [Indexed: 01/04/2023]
Abstract
CodY and (p)ppGpp synthetases are two important global regulators of bacteria. In some pathogens, such as Listeria monocytogenes, the GTP pool links these two regulatory systems, and introducing a codY mutant into the ΔrelA strain restored the pathogenicity of the attenuated ΔrelA mutant. In previous studies, we identified the (p)ppGpp synthetases (RelA and RelQ) and CodY of Streptococcus suis. To understand the interrelationships between these two regulators in S. suis, a ΔrelAΔrelQΔcodY mutant was constructed, and its growth, morphology, and pathogenicity were evaluated. Compared with ΔrelAΔrelQ, ΔcodY, its growth was very slow, but its chain length was partly restored to the wild-type length and its capsule became thick and rough. The adherence, invasion ability, and resistance to whole-blood killing in vitro of ΔrelAΔrelQΔcodY and its lethality and colonization ability in mice were clearly reduced, which differs from the effects of these mutations in L. monocytogenes. An analysis of gene expression showed that CodY interacted with the relA promoter in a GTP-independent manner to positively regulate the expression of relA. The introduction of a codY mutant into the ΔrelAΔrelQ strain further reduced the expression of virulence factors, which suggests a novel interaction between the (p)ppGpp synthetases and CodY. This study extends our understanding of the relationship between the (p)ppGpp-mediated stringent response and the regulation of CodY in S. suis.
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19
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Increased Mortality in Mice following Immunoprophylaxis Therapy with High Dosage of Nicotinamide in Burkholderia Persistent Infections. Infect Immun 2018; 87:IAI.00592-18. [PMID: 30323029 PMCID: PMC6300628 DOI: 10.1128/iai.00592-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/09/2018] [Indexed: 12/27/2022] Open
Abstract
Bacterial persistence, known as noninherited antibacterial resistance, is a factor contributing to the establishment of long-lasting chronic bacterial infections. In this study, we examined the ability of nicotinamide (NA) to potentiate the activity of different classes of antibiotics against Burkholderia thailandensis persister cells. Bacterial persistence, known as noninherited antibacterial resistance, is a factor contributing to the establishment of long-lasting chronic bacterial infections. In this study, we examined the ability of nicotinamide (NA) to potentiate the activity of different classes of antibiotics against Burkholderia thailandensis persister cells. Here we demonstrate that addition of NA in in vitro models of B. thailandensis infection resulted in a significant depletion of the persister population in response to various classes of antibiotics. We applied microfluidic bioreactors with a continuous medium flow to study the effect of supplementation with an NA gradient on the recovery of B. thailandensis persister populations. A coculture of human neutrophils preactivated with 50 µM NA and B. thailandensis resulted in the most efficient reduction in the persister population. Applying single-cell RNA fluorescence in situ hybridization analysis and quantitative PCR, we found that NA inhibited gene expression of the stringent response regulator relA, implicated in the regulation of the persister metabolic state. We also demonstrate that a therapeutic dose of NA (250 mg/kg of body weight), previously applied as immunoprophylaxis against antibiotic-resistant bacterial species, produced adverse effects in an in vivo murine model of infection with the highly pathogenic bacterium Burkholderia pseudomallei, indicating that therapeutic dose and metabolite effects have to be carefully evaluated and tailored for every case of potential clinical application.
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Functional characterization of murB-potABCD operon for polyamine uptake and peptidoglycan synthesis in Streptococcus suis. Microbiol Res 2018; 207:177-187. [DOI: 10.1016/j.micres.2017.11.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 10/11/2017] [Accepted: 11/12/2017] [Indexed: 01/27/2023]
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21
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Sitkiewicz I. How to become a killer, or is it all accidental? Virulence strategies in oral streptococci. Mol Oral Microbiol 2017; 33:1-12. [PMID: 28727895 DOI: 10.1111/omi.12192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2017] [Indexed: 01/03/2023]
Abstract
Streptococci are a diverse group of Gram-positive microorganisms sharing common virulence traits and similar strategies to escape the oral niche and establish an infection in other parts of the host organism. Invasive infection with oral streptococci is "a perfect storm" that requires the concerted action of multiple biotic and abiotic factors. Our understanding of streptococcal pathogenicity and infectivity should probably be less mechanistic and driven not only by the identification of novel virulence factors. The observed diversity of the genus, including the range of virulence and pathogenicity mechanisms, is most likely the result of interspecies interactions, a massive horizontal gene transfer between streptococci within a shared oral niche, recombination events, selection of specialized clones, and modification of regulatory circuits. Selective pressure by the host and bacterial communities is a driving force for the selection of virulence traits and shaping the streptococcal genome. Global regulatory events driving niche adaptation and interactions with bacterial communities and the host steer research interests towards attempts to define the oral interactome on the transcriptional level and define signal cross-feeding and co-expression and co-regulation of virulence genes.
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Affiliation(s)
- I Sitkiewicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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