101
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Bínová E, Bína D, Nohýnková E. DNA content in Acanthamoeba during two stress defense reactions: Encystation, pseudocyst formation and cell cycle. Eur J Protistol 2020; 77:125745. [PMID: 33218872 DOI: 10.1016/j.ejop.2020.125745] [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: 06/03/2020] [Revised: 08/22/2020] [Accepted: 10/19/2020] [Indexed: 12/01/2022]
Abstract
During environmental stress, the vegetative cells of the facultative pathogenic amoeba Acanthamoeba castellanii reversibly differentiate into resistant dormant stages, namely, cysts or pseudocysts. The type of resistant stage depends on the nature and duration of the stressor. Cell differentiation is accompanied by changes in morphology and cellular metabolism. Moreover, cell differentiation is also expected to be closely linked to the regulation of the cell cycle and, thus, to cellular DNA content. While the existence of the resistant stages in A. castellanii is well known, there is no consensus regarding the relationship between differentiation and cell cycle progression. In the present work, we used flow cytometry analysis to explore the changes in the DNA content during Acanthamoeba encystation and pseudocyst formation. Our results strongly indicate that A. castellanii enters encystation from the G2 phase of the cell cycle. In contrast, differentiation into pseudocysts can begin in the G1 and G2 phases. In addition, we present a phylogenetic analysis and classification of the main cell cycle regulators, namely, cyclin-dependent kinases and cyclins that are found in the genome of A. castellanii.
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Affiliation(s)
- Eva Bínová
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Studnickova 7, 128 00 Prague 2, Czech Republic
| | - David Bína
- Faculty of Science, University of South Bohemia, Branišovská 1760 and The Czech Academy of Sciences, Biology Centre, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Eva Nohýnková
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Studnickova 7, 128 00 Prague 2, Czech Republic.
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102
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Jia Y, Yu C, Fan J, Fu Y, Ye Z, Guo X, Xu Y, Shen C. Alterations in the Cell Wall of Rhodococcus biphenylivorans Under Norfloxacin Stress. Front Microbiol 2020; 11:554957. [PMID: 33123102 PMCID: PMC7573542 DOI: 10.3389/fmicb.2020.554957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/14/2020] [Indexed: 01/20/2023] Open
Abstract
Many microorganisms can enter a viable but non-culturable (VBNC) state under various environmental stresses, while they can also resuscitate when the surroundings turn to suitable conditions. Cell walls play a vital role in maintaining cellular integrity and protecting cells from ambient threats. Here, we investigated the alterations in the cell wall of Rhodococcus biphenylivorans TG9 at VBNC state under norfloxacin stress and then at resuscitated state in fresh lysogeny broth medium. Electron microscopy analyses presented that TG9 in the VBNC state had a thicker and rougher cell wall than that in exponential phase or resuscitated state. Meanwhile, the results from infrared spectroscopy also showed that its VBNC state has different peptidoglycan structures in the cell wall. Moreover, in the VBNC cells the gene expressions related to cell wall synthesis and remodeling maintain a relatively high level. It indicates that the morphological variations of TG9 at the VBNC state might result from kinetic changes in the cell wall synthesis and remodeling. As a consequence, the alterations in the cell wall of VBNC TG9 may somewhat account for its tolerance mechanisms to antibiotic treatment.
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Affiliation(s)
- Yangyang Jia
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Chungui Yu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jiahui Fan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yulong Fu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Zhe Ye
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoguang Guo
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Ying Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
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103
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Vargas-Blanco DA, Shell SS. Regulation of mRNA Stability During Bacterial Stress Responses. Front Microbiol 2020; 11:2111. [PMID: 33013770 PMCID: PMC7509114 DOI: 10.3389/fmicb.2020.02111] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
Bacteria have a remarkable ability to sense environmental changes, swiftly regulating their transcriptional and posttranscriptional machinery as a response. Under conditions that cause growth to slow or stop, bacteria typically stabilize their transcriptomes in what has been shown to be a conserved stress response. In recent years, diverse studies have elucidated many of the mechanisms underlying mRNA degradation, yet an understanding of the regulation of mRNA degradation under stress conditions remains elusive. In this review we discuss the diverse mechanisms that have been shown to affect mRNA stability in bacteria. While many of these mechanisms are transcript-specific, they provide insight into possible mechanisms of global mRNA stabilization. To that end, we have compiled information on how mRNA fate is affected by RNA secondary structures; interaction with ribosomes, RNA binding proteins, and small RNAs; RNA base modifications; the chemical nature of 5' ends; activity and concentration of RNases and other degradation proteins; mRNA and RNase localization; and the stringent response. We also provide an analysis of reported relationships between mRNA abundance and mRNA stability, and discuss the importance of stress-associated mRNA stabilization as a potential target for therapeutic development.
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Affiliation(s)
- Diego A Vargas-Blanco
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Scarlet S Shell
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States.,Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
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104
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Buongiorno J, Sipes K, Wasmund K, Loy A, Lloyd KG. Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PLoS One 2020; 15:e0234839. [PMID: 32853201 PMCID: PMC7451513 DOI: 10.1371/journal.pone.0234839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022] Open
Abstract
Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.
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Affiliation(s)
- Joy Buongiorno
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Katie Sipes
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Karen G. Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
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105
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Monem S, Furmanek-Blaszk B, Łupkowska A, Kuczyńska-Wiśnik D, Stojowska-Swędrzyńska K, Laskowska E. Mechanisms Protecting Acinetobacter baumannii against Multiple Stresses Triggered by the Host Immune Response, Antibiotics and Outside-Host Environment. Int J Mol Sci 2020; 21:E5498. [PMID: 32752093 PMCID: PMC7432025 DOI: 10.3390/ijms21155498] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023] Open
Abstract
Acinetobacter baumannii is considered one of the most persistent pathogens responsible for nosocomial infections. Due to the emergence of multidrug resistant strains, as well as high morbidity and mortality caused by this pathogen, A. baumannii was placed on the World Health Organization (WHO) drug-resistant bacteria and antimicrobial resistance research priority list. This review summarizes current studies on mechanisms that protect A. baumannii against multiple stresses caused by the host immune response, outside host environment, and antibiotic treatment. We particularly focus on the ability of A. baumannii to survive long-term desiccation on abiotic surfaces and the population heterogeneity in A. baumannii biofilms. Insight into these protective mechanisms may provide clues for the development of new strategies to fight multidrug resistant strains of A. baumannii.
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Affiliation(s)
- Soroosh Monem
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (S.M.); (A.Ł.); (D.K.-W.); (K.S.-S.)
| | - Beata Furmanek-Blaszk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| | - Adrianna Łupkowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (S.M.); (A.Ł.); (D.K.-W.); (K.S.-S.)
| | - Dorota Kuczyńska-Wiśnik
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (S.M.); (A.Ł.); (D.K.-W.); (K.S.-S.)
| | - Karolina Stojowska-Swędrzyńska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (S.M.); (A.Ł.); (D.K.-W.); (K.S.-S.)
| | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (S.M.); (A.Ł.); (D.K.-W.); (K.S.-S.)
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106
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Gunderson EL, Vogel I, Chappell L, Bulman CA, Lim KC, Luo M, Whitman JD, Franklin C, Choi YJ, Lefoulon E, Clark T, Beerntsen B, Slatko B, Mitreva M, Sullivan W, Sakanari JA. The endosymbiont Wolbachia rebounds following antibiotic treatment. PLoS Pathog 2020; 16:e1008623. [PMID: 32639986 PMCID: PMC7371230 DOI: 10.1371/journal.ppat.1008623] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/20/2020] [Accepted: 05/13/2020] [Indexed: 12/20/2022] Open
Abstract
Antibiotic treatment has emerged as a promising strategy to sterilize and kill filarial nematodes due to their dependence on their endosymbiotic bacteria, Wolbachia. Several studies have shown that novel and FDA-approved antibiotics are efficacious at depleting the filarial nematodes of their endosymbiont, thus reducing female fecundity. However, it remains unclear if antibiotics can permanently deplete Wolbachia and cause sterility for the lifespan of the adult worms. Concerns about resistance arising from mass drug administration necessitate a careful exploration of potential Wolbachia recrudescence. In the present study, we investigated the long-term effects of the FDA-approved antibiotic, rifampicin, in the Brugia pahangi jird model of infection. Initially, rifampicin treatment depleted Wolbachia in adult worms and simultaneously impaired female worm fecundity. However, during an 8-month washout period, Wolbachia titers rebounded and embryogenesis returned to normal. Genome sequence analyses of Wolbachia revealed that despite the population bottleneck and recovery, no genetic changes occurred that could account for the rebound. Clusters of densely packed Wolbachia within the worm's ovarian tissues were observed by confocal microscopy and remained in worms treated with rifampicin, suggesting that they may serve as privileged sites that allow Wolbachia to persist in worms while treated with antibiotic. To our knowledge, these clusters have not been previously described and may be the source of the Wolbachia rebound.
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Affiliation(s)
- Emma L. Gunderson
- Dept. of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, California, United States of America
| | - Ian Vogel
- Dept. of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, California, United States of America
| | - Laura Chappell
- Dept. of Molecular, Cell and Developmental Biology; University of California, Santa Cruz; Santa Cruz, California, United States of America
| | - Christina A. Bulman
- Dept. of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, California, United States of America
| | - K. C. Lim
- Dept. of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, California, United States of America
| | - Mona Luo
- Dept. of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, California, United States of America
| | - Jeffrey D. Whitman
- Dept. of Laboratory Medicine; University of California, San Francisco; San Francisco, California, United States of America
| | - Chris Franklin
- Dept. of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, California, United States of America
| | - Young-Jun Choi
- Division of Infectious Diseases; Washington University School of Medicine, St. Louis; St. Louis, Missouri, United States of America
| | - Emilie Lefoulon
- Molecular Parasitology Division; New England BioLabs; Ipswich, Massachusetts, United States of America
| | - Travis Clark
- Veterinary Pathobiology; University of Missouri-Columbia; Columbia, Missouri, United States of America
| | - Brenda Beerntsen
- Veterinary Pathobiology; University of Missouri-Columbia; Columbia, Missouri, United States of America
| | - Barton Slatko
- Molecular Parasitology Division; New England BioLabs; Ipswich, Massachusetts, United States of America
| | - Makedonka Mitreva
- Division of Infectious Diseases; Washington University School of Medicine, St. Louis; St. Louis, Missouri, United States of America
| | - William Sullivan
- Dept. of Molecular, Cell and Developmental Biology; University of California, Santa Cruz; Santa Cruz, California, United States of America
| | - Judy A. Sakanari
- Dept. of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, California, United States of America
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107
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The alarmones (p)ppGpp directly regulate translation initiation during entry into quiescence. Proc Natl Acad Sci U S A 2020; 117:15565-15572. [PMID: 32576694 DOI: 10.1073/pnas.1920013117] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Many bacteria exist in a state of metabolic quiescence where energy consumption must be minimized so as to maximize available resources over a potentially extended period of time. As protein synthesis is the most energy intensive metabolic process in a bacterial cell, it would be an appropriate target for down-regulation during the transition from growth to quiescence. We observe that when Bacillus subtilis exits rapid growth, a subpopulation of cells emerges with very low protein synthetic activity. This phenotypic heterogeneity requires the production of the nucleotides (p)ppGpp, which we show are sufficient to inhibit protein synthesis in vivo. We then show that one of these molecules, ppGpp, inhibits protein synthesis by preventing the allosteric activation of the essential GTPase Initiation Factor 2 (IF2) during translation initiation. Finally, we demonstrate that the observed attenuation of protein synthesis during the entry into quiescence is a consequence of the direct interaction of (p)ppGpp and IF2.
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108
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Nitrite modulates aminoglycoside tolerance by inhibiting cytochrome heme-copper oxidase in bacteria. Commun Biol 2020; 3:269. [PMID: 32461576 PMCID: PMC7253457 DOI: 10.1038/s42003-020-0991-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/05/2020] [Indexed: 01/23/2023] Open
Abstract
As a bacteriostatic agent, nitrite has been used in food preservation for centuries. When used in combination with antibiotics, nitrite is reported to work either cooperatively or antagonistically. However, the mechanism underlying these effects remains largely unknown. Here we show that nitrite mediates tolerance to aminoglycosides in both Gram-negative and Gram-positive bacteria, but has little interaction with other types of antibiotics. Nitrite directly and mainly inhibits cytochrome heme-copper oxidases (HCOs), and by doing so, the membrane potential is compromised, blocking uptake of aminoglycosides. In contrast, reduced respiration (oxygen consumption rate) resulting from nitrite inhibition is not critical for aminoglycoside tolerance. While our data indicate that nitrite is a promising antimicrobial agent targeting HCOs, cautions should be taken when used with other antibiotics, aminoglycosides in particular.
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109
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Ribosome Dimerization Protects the Small Subunit. J Bacteriol 2020; 202:JB.00009-20. [PMID: 32123037 PMCID: PMC7186458 DOI: 10.1128/jb.00009-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 02/25/2020] [Indexed: 01/21/2023] Open
Abstract
When nutrients become scarce, bacteria can enter an extended state of quiescence. A major challenge of this state is how to preserve ribosomes for the return to favorable conditions. Here, we show that the ribosome dimerization protein hibernation-promoting factor (HPF) functions to protect essential ribosomal proteins. Ribosomes isolated from strains lacking HPF (Δhpf) or encoding a mutant allele of HPF that binds the ribosome but does not mediate dimerization were substantially depleted of the small subunit proteins S2 and S3. Strikingly, these proteins are located directly at the ribosome dimer interface. We used single-particle cryo-electron microscopy (cryo-EM) to further characterize these ribosomes and observed that a high percentage of ribosomes were missing S2, S3, or both. These data support a model in which the ribosome dimerization activity of HPF evolved to protect labile proteins that are essential for ribosome function. HPF is almost universally conserved in bacteria, and HPF deletions in diverse species exhibit decreased viability during starvation. Our data provide mechanistic insight into this phenotype and establish a mechanism for how HPF protects ribosomes during quiescence.IMPORTANCE The formation of ribosome dimers during periods of dormancy is widespread among bacteria. Dimerization is typically mediated by a single protein, hibernation-promoting factor (HPF). Bacteria lacking HPF exhibit strong defects in viability and pathogenesis and, in some species, extreme loss of rRNA. The mechanistic basis of these phenotypes has not been determined. Here, we report that HPF from the Gram-positive bacterium Bacillus subtilis preserves ribosomes by preventing the loss of essential ribosomal proteins at the dimer interface. This protection may explain phenotypes associated with the loss of HPF, since ribosome protection would aid survival during nutrient limitation and impart a strong selective advantage when the bacterial cell rapidly reinitiates growth in the presence of sufficient nutrients.
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110
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Altamura F, Rajesh R, Catta-Preta CMC, Moretti NS, Cestari I. The current drug discovery landscape for trypanosomiasis and leishmaniasis: Challenges and strategies to identify drug targets. Drug Dev Res 2020; 83:225-252. [PMID: 32249457 DOI: 10.1002/ddr.21664] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/05/2020] [Accepted: 03/13/2020] [Indexed: 12/11/2022]
Abstract
Human trypanosomiasis and leishmaniasis are vector-borne neglected tropical diseases caused by infection with the protozoan parasites Trypanosoma spp. and Leishmania spp., respectively. Once restricted to endemic areas, these diseases are now distributed worldwide due to human migration, climate change, and anthropogenic disturbance, causing significant health and economic burden globally. The current chemotherapy used to treat these diseases has limited efficacy, and drug resistance is spreading. Hence, new drugs are urgently needed. Phenotypic compound screenings have prevailed as the leading method to discover new drug candidates against these diseases. However, the publication of the complete genome sequences of multiple strains, advances in the application of CRISPR/Cas9 technology, and in vivo bioluminescence-based imaging have set the stage for advancing target-based drug discovery. This review analyses the limitations of the narrow pool of available drugs presently used for treating these diseases. It describes the current drug-based clinical trials highlighting the most promising leads. Furthermore, the review presents a focused discussion on the most important biological and pharmacological challenges that target-based drug discovery programs must overcome to advance drug candidates. Finally, it examines the advantages and limitations of modern research tools designed to identify and validate essential genes as drug targets, including genomic editing applications and in vivo imaging.
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Affiliation(s)
- Fernando Altamura
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
| | - Rishi Rajesh
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
| | | | - Nilmar S Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Igor Cestari
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
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111
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Takeuchi T, Sears BB, Lindeboom C, Lin YT, Fekaris N, Zienkiewicz K, Zienkiewicz A, Poliner E, Benning C. Chlamydomonas CHT7 Is Required for an Effective Quiescent State by Regulating Nutrient-Responsive Cell Cycle Gene Expression. THE PLANT CELL 2020; 32:1240-1269. [PMID: 32001503 PMCID: PMC7145468 DOI: 10.1105/tpc.19.00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/07/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
COMPROMISED HYDROLYSIS OF TRIACYLGLYCEROLS7 (CHT7) in Chlamydomonas (Chlamydomonas reinhardtii) was previously shown to affect the transcription of a subset of genes during nitrogen (N)-replete growth and following N refeeding. Here, we show that an extensive derepression of genes involved in DNA metabolism and cell cycle-related processes, as well as downregulation of genes encoding oxidoreductases and nutrient transporters, occurs in the cht7 mutant during N deprivation. Cellular mutant phenotypes are consistent with the observed transcriptome misregulation, as cht7 cells fail to properly arrest growth, nuclear replication, and cell division following N deprivation. Reduction in cht7 colony formation following N refeeding is explained by its compromised viability during N deprivation and by the occurrence of abortive divisions during N refeeding. Surprisingly, the largely unstructured C-terminal half of CHT7 with predicted protein binding domains, but not the canonical CXC DNA binding domain, is essential for the ability of CHT7 to form stable complexes and reverse the cellular phenotypes and transcription levels in the cht7 mutant. Hence, although lacking the presumed DNA binding domain, CHT7 modulates the expression of cell cycle genes in response to N availability, which is essential for establishing an effective quiescent state and the coordinated resumption of growth following N refeeding.
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Affiliation(s)
- Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Barbara B Sears
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Chase Lindeboom
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Yang-Tsung Lin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Nicholas Fekaris
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Krzysztof Zienkiewicz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Centre of Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
| | - Agnieszka Zienkiewicz
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Centre of Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
| | - Eric Poliner
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
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112
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Munkager V, Vestergård M, Priemé A, Altenburger A, de Visser E, Johansen JL, Ekelund F. AgNO 3 Sterilizes Grains of Barley ( Hordeum vulgare) without Inhibiting Germination-A Necessary Tool for Plant-Microbiome Research. PLANTS 2020; 9:plants9030372. [PMID: 32192219 PMCID: PMC7154866 DOI: 10.3390/plants9030372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 11/16/2022]
Abstract
To understand and manipulate the interactions between plants and microorganisms, sterile seeds are a necessity. The seed microbiome (inside and surface microorganisms) is unknown for most plant species and seed-borne microorganisms can persist and transfer to the seedling and rhizosphere, thereby obscuring the effects that purposely introduced microorganisms have on plants. This necessitates that these unidentified, seed-borne microorganisms are removed before seeds are used for studies on plant–microbiome interactions. Unfortunately, there is no single, standardized protocol for seed sterilization, hampering progress in experimental plant growth promotion and our study shows that commonly applied sterilization protocols for barley grains using H2O2, NaClO, and AgNO3 yielded insufficient sterilization. We therefore developed a sterilization protocol with AgNO3 by testing several concentrations of AgNO3 and added two additional steps: Soaking the grains in water before the sterilization and rinsing with salt water (1% (w/w) NaCl) after the sterilization. The most efficient sterilization protocol was to soak the grains, sterilize with 10% (w/w) AgNO3, and to rinse with salt water. By following those three steps, 97% of the grains had no culturable, viable microorganism after 21 days based on microscopic inspection. The protocol left small quantities of AgNO3 residue on the grain, maintained germination percentage similar to unsterilized grains, and plant biomass was unaltered. Hence, our protocol using AgNO3 can be used successfully for experiments on plant–microbiome interactions.
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Affiliation(s)
- Victoria Munkager
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark (J.L.J.)
- Correspondence: ; Tel.: +45-27-12-16-33
| | - Mette Vestergård
- Department of Agroecology, Aarhus University, 4200 Slagelse, Denmark
| | - Anders Priemé
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark (J.L.J.)
| | - Andreas Altenburger
- The Arctic University Museum of Norway, UiT—The Arctic University of Norway, 9006 Tromsø, Norway
| | - Eva de Visser
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark (J.L.J.)
| | | | - Flemming Ekelund
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark (J.L.J.)
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113
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Martínez SR, Aiassa V, Sola C, Becerra MC. Oxidative stress response in reference and clinical Staphylococcus aureus strains under Linezolid exposure. J Glob Antimicrob Resist 2020; 22:257-262. [PMID: 32169679 DOI: 10.1016/j.jgar.2020.02.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/12/2020] [Accepted: 02/21/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) strains are some of the most widespread pathogens with multi-resistant to antimicrobial agents (AA). AA provoke several changes inside bacteria, which cannot be solely explained by the main mechanisms of action reported. OBJECTIVE The role of oxidative stress in bacteria exposed to bacteriostatic AA has not been widely studied; hence, the aim of our work was to investigate the effect of linezolid (LZD) on S. aureus strains. METHODS Oxidative stress markers, such as superoxide dismutase (SOD) enzyme activity, the global antioxidant response, advanced oxidation protein products (AOPP) and basal levels of glutathione in 28 clinical and 2 reference strains were measured. RESULTS AND CONCLUSIONS We identified 10 of 30 strains showing a slight increase in reactive species under LZD treatment with respect to the untreated control (between 22% and 56%). Higher generation was detected in clinical strains compared with the reference strains; however, the impact on the antioxidant response was not significant, and the oxidized protein levels were almost undetectable. The strains exposed to this oxazolidinone did not suffer acute oxidative stress. This is the first work reporting the behaviour of clinical and reference strains of S. aureus exposed to LZD, showing negligible oxidative stress.
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Affiliation(s)
- Sol Romina Martínez
- InstitutoMultidisciplinario de Biología Vegetal (IMBIV), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina.
| | - Virginia Aiassa
- Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina.
| | - Claudia Sola
- Departamento Bioquímica Clínica, Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI) CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina.
| | - María Cecilia Becerra
- InstitutoMultidisciplinario de Biología Vegetal (IMBIV), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina.
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114
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Heat-shock proteases promote survival of Pseudomonas aeruginosa during growth arrest. Proc Natl Acad Sci U S A 2020; 117:4358-4367. [PMID: 32029587 DOI: 10.1073/pnas.1912082117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
When nutrients in their environment are exhausted, bacterial cells become arrested for growth. During these periods, a primary challenge is maintaining cellular integrity with a reduced capacity for renewal or repair. Here, we show that the heat-shock protease FtsH is generally required for growth arrest survival of Pseudomonas aeruginosa, and that this requirement is independent of a role in regulating lipopolysaccharide synthesis, as has been suggested for Escherichia coli We find that ftsH interacts with diverse genes during growth and overlaps functionally with the other heat-shock protease-encoding genes hslVU, lon, and clpXP to promote survival during growth arrest. Systematic deletion of the heat-shock protease-encoding genes reveals that the proteases function hierarchically during growth arrest, with FtsH and ClpXP having primary, nonredundant roles, and HslVU and Lon deploying a secondary response to aging stress. This hierarchy is partially conserved during growth at high temperature and alkaline pH, suggesting that heat, pH, and growth arrest effectively impose a similar type of proteostatic stress at the cellular level. In support of this inference, heat and growth arrest act synergistically to kill cells, and protein aggregation appears to occur more rapidly in protease mutants during growth arrest and correlates with the onset of cell death. Our findings suggest that protein aggregation is a major driver of aging and cell death during growth arrest, and that coordinated activity of the heat-shock response is required to ensure ongoing protein quality control in the absence of growth.
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115
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Dal Co A, van Vliet S, Ackermann M. Emergent microscale gradients give rise to metabolic cross-feeding and antibiotic tolerance in clonal bacterial populations. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190080. [PMID: 31587651 PMCID: PMC6792440 DOI: 10.1098/rstb.2019.0080] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2019] [Indexed: 12/18/2022] Open
Abstract
Bacteria often live in spatially structured groups such as biofilms. In these groups, cells can collectively generate gradients through the uptake and release of compounds. In turn, individual cells adapt their activities to the environment shaped by the whole group. Here, we studied how these processes can generate phenotypic variation in clonal populations and how this variation contributes to the resilience of the population to antibiotics. We grew two-dimensional populations of Escherichia coli in microfluidic chambers where limiting amounts of glucose were supplied from one side. We found that the collective metabolic activity of cells created microscale gradients where nutrient concentration varied over a few cell lengths. As a result, growth rates and gene expression levels varied strongly between neighbouring cells. Furthermore, we found evidence for a metabolic cross-feeding interaction between glucose-fermenting and acetate-respiring subpopulations. Finally, we found that subpopulations of cells were able to survive an antibiotic pulse that was lethal in well-mixed conditions, likely due to the presence of a slow-growing subpopulation. Our work shows that emergent metabolic gradients can have important consequences for the functionality of bacterial populations as they create opportunities for metabolic interactions and increase the populations' tolerance to environmental stressors. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- Alma Dal Co
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Department of Environmental Microbiology, Eawag, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Simon van Vliet
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Department of Environmental Microbiology, Eawag, Überlandstrasse 133, 8600 Dübendorf, Switzerland
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia,CanadaV6T 1Z4
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Department of Environmental Microbiology, Eawag, Überlandstrasse 133, 8600 Dübendorf, Switzerland
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116
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Hards K, Adolph C, Harold LK, McNeil MB, Cheung CY, Jinich A, Rhee KY, Cook GM. Two for the price of one: Attacking the energetic-metabolic hub of mycobacteria to produce new chemotherapeutic agents. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 152:35-44. [PMID: 31733221 DOI: 10.1016/j.pbiomolbio.2019.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022]
Abstract
Cellular bioenergetics is an area showing promise for the development of new antimicrobials, antimalarials and cancer therapy. Enzymes involved in central carbon metabolism and energy generation are essential mediators of bacterial physiology, persistence and pathogenicity, lending themselves natural interest for drug discovery. In particular, succinate and malate are two major focal points in both the central carbon metabolism and the respiratory chain of Mycobacterium tuberculosis. Both serve as direct links between the citric acid cycle and the respiratory chain due to the quinone-linked reactions of succinate dehydrogenase, fumarate reductase and malate:quinone oxidoreductase. Inhibitors against these enzymes therefore hold the promise of disrupting two distinct, but essential, cellular processes at the same time. In this review, we discuss the roles and unique adaptations of these enzymes and critically evaluate the role that future inhibitors of these complexes could play in the bioenergetics target space.
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Affiliation(s)
- Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand.
| | - Cara Adolph
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand
| | - Liam K Harold
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand
| | - Adrian Jinich
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand.
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117
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Antimicrobial Treatment Provides a Competitive Advantage to Mycobacterium abscessus in a Dual-Species Biofilm with Pseudomonas aeruginosa. Antimicrob Agents Chemother 2019; 63:AAC.01547-19. [PMID: 31451500 DOI: 10.1128/aac.01547-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 08/13/2019] [Indexed: 12/14/2022] Open
Abstract
The physiological factors that contribute to Mycobacterium abscessus lung infections remain unclear. We determined whether antibiotic treatment targeting a major cystic fibrosis pathogen (i.e., Pseudomonas aeruginosa) could provide the ideal conditions for the establishment of M. abscessus infection. Our data showed that P. aeruginosa inhibited M. abscessus biofilm formation under control conditions and that antimicrobial therapy selectively targeting P. aeruginosa diminished this competitive interaction, thereby increasing M. abscessus survival.
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118
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Whitfield DL, Sharma G, Smaldone GT, Singer M. Peripheral rods: a specialized developmental cell type in Myxococcus xanthus. Genomics 2019; 112:1588-1597. [PMID: 31605730 DOI: 10.1016/j.ygeno.2019.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/13/2019] [Accepted: 09/11/2019] [Indexed: 01/08/2023]
Abstract
In response to nutrient deprivation, the ubiquitous Gram-negative soil bacterium Myxococcus xanthus undergoes a well-characterized developmental response, resulting in the formation of a multicellular fruiting body. The center of the fruiting body consists of myxospores; surrounding this structure are rod-shaped peripheral cells. Unlike spores, the peripheral rods are a metabolically active cell type that inhabits nutrient-deprived environments. The survival characteristics exhibited by peripheral rods, protection from oxidative stress and heat shock, are common survival characteristics exhibited by cells in stationary phase including modifications to morphology and metabolism. Vegetative M. xanthus cells undergo a number of physiological changes during the transition into stationary phase similar to other proteobacteria. In M. xanthus, stationary-phase cells are not considered a component of the developmental response and occur when cells are grown on nutrient-rich plates or in dispersed aqueous media. However, this cell type is not routinely studied and little of its physiology is known. Similarities between these two stress-induced cell types led to the question of whether peripheral rods are actually a distinct developmental cell type or simply cells in stationary phase. In this study, we examine the transcriptome of peripheral rods and its relationship to development. This work demonstrates that peripheral rods are in fact a distinct developmentally differentiated cell type. Although peripheral rods and stationary phase cells display similar characteristics, each transcriptomic pattern is unique and quite different from that of any other M. xanthus cell type.
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Affiliation(s)
- Damion L Whitfield
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA.
| | - Gaurav Sharma
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Gregory T Smaldone
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Mitchell Singer
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA.
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119
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Kunadiya MB, Dunstan WD, White D, Hardy GESJ, Grigg AH, Burgess TI. A qPCR Assay for the Detection of Phytophthora cinnamomi Including an mRNA Protocol Designed to Establish Propagule Viability in Environmental Samples. PLANT DISEASE 2019; 103:2443-2450. [PMID: 31313641 DOI: 10.1094/pdis-09-18-1641-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phytophthora cinnamomi causes root and collar rot in many plant species in natural ecosystems and horticulture. A species-specific primer and probe PCIN5 were designed based on a mitochondrial locus encoding subunit 2 of cytochrome c oxidase (cox2). Eight PCR primers, including three forward and five reverse, were designed and tested in all possible combinations. Annealing temperatures were optimized for each primer pair set to maximize both specificity and sensitivity. Each set was tested against P. cinnamomi and two closely related clade 7 species, P. parvispora and P. niederhauseri. From these tests, five primer pairs were selected based on specificity and, with a species-specific P. cinnamomi probe, used to develop quantitative real-time PCR (qPCR) assays. The specificity of the two most sensitive qPCR assays was confirmed using the genomic DNA of 29 Phytophthora isolates, including 17 isolates of 11 species from clade 7, and representative species from nine other clades (all except clade 3). The assay was able to detect as little as 150 ag of P. cinnamomi DNA and showed no cross-reaction with other Phytophthora species, except for P. parvispora, a very closely related species to P. cinnamomi, which showed late amplification at high DNA concentrations. The efficiency of the qPCR protocol was evaluated with environmental samples including roots and associated soil from plants artificially infected with P. cinnamomi. Different RNA isolation kits were tested and evaluated for their performance in the isolation of RNA from environmental samples, followed by cDNA synthesis, and qPCR assay. Finally, a protocol was recommended for determining the presence of P. cinnamomi in recalcitrant environmental samples.
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Affiliation(s)
- Manisha B Kunadiya
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - William D Dunstan
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Diane White
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Giles E St J Hardy
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Andrew H Grigg
- Alcoa of Australia Ltd., Huntly Mine, Pinjarra, WA 6208, Australia
| | - Treena I Burgess
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
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120
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Patel HV, Li M, Seeliger JC. Opportunities and Challenges in Activity-Based Protein Profiling of Mycobacteria. Curr Top Microbiol Immunol 2019; 420:49-72. [PMID: 30178262 DOI: 10.1007/82_2018_125] [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: 10/28/2022]
Abstract
Mycobacteria, from saprophytic to pathogenic species, encounter diverse environments that demand metabolic versatility and rapid adaptation from these bacteria for their survival. The human pathogen Mycobacterium tuberculosis, for example, can enter a reversible state of dormancy in which it is metabolically active, but does not increase in number, and which is believed to enable its survival in the human host for years, with attendant risk for reactivation to active tuberculosis. Driven by the need to combat mycobacterial diseases like tuberculosis, efforts to understand such adaptations have benefitted in recent years from application of activity-based probes. These studies have been inspired by the potential of these chemical tools to uncover protein function for previously unannotated proteins, track shifts in protein activity as a function of environment, and provide a streamlined method for screening and developing inhibitors. Here we seek to contextualize progress thus far with achieving these goals and highlight the unique challenges and opportunities for activity-based probes to further our understanding of protein function and regulation, bacterial physiology, and antibiotic development.
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Affiliation(s)
- Hiren V Patel
- Department of Molecular Genetics and Microbiology, Stony Brook University, 11794, Stony Brook, NY, USA
| | - Michael Li
- Department of Pharmacological Sciences, Stony Brook University, 11794, Stony Brook, NY, USA
| | - Jessica C Seeliger
- Department of Pharmacological Sciences, Stony Brook University, 11794, Stony Brook, NY, USA.
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121
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Hommel B, Sturny-Leclère A, Volant S, Veluppillai N, Duchateau M, Yu CH, Hourdel V, Varet H, Matondo M, Perfect JR, Casadevall A, Dromer F, Alanio A. Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype. PLoS Pathog 2019; 15:e1007945. [PMID: 31356623 PMCID: PMC6687208 DOI: 10.1371/journal.ppat.1007945] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/08/2019] [Accepted: 06/27/2019] [Indexed: 01/22/2023] Open
Abstract
Metabolically quiescent pathogens can persist in a viable non-replicating state for months or even years. For certain infectious diseases, such as tuberculosis, cryptococcosis, histoplasmosis, latent infection is a corollary of this dormant state, which has the risk for reactivation and clinical disease. During murine cryptococcosis and macrophage uptake, stress and host immunity induce Cryptococcus neoformans heterogeneity with the generation of a sub-population of yeasts that manifests a phenotype compatible with dormancy (low stress response, latency of growth). In this subpopulation, mitochondrial transcriptional activity is regulated and this phenotype has been considered as a hallmark of quiescence in stem cells. Based on these findings, we worked to reproduce this phenotype in vitro and then standardize the experimental conditions to consistently generate this dormancy in C. neoformans. We found that incubation of stationary phase yeasts (STAT) in nutriment limited conditions and hypoxia for 8 days (8D-HYPOx) was able to produced cells that mimic the phenotype obtained in vivo. In these conditions, mortality and/or apoptosis occurred in less than 5% of the yeasts compared to 30-40% of apoptotic or dead yeasts upon incubation in normoxia (8D-NORMOx). Yeasts in 8D-HYPOx harbored a lower stress response, delayed growth and less that 1% of culturability on agar plates, suggesting that these yeasts are viable but non culturable cells (VBNC). These VBNC were able to reactivate in the presence of pantothenic acid, a vitamin that is known to be involved in quorum sensing and a precursor of acetyl-CoA. Global metabolism of 8D-HYPOx cells showed some specific requirements and was globally shut down compared to 8D-NORMOx and STAT conditions. Mitochondrial analyses showed that the mitochondrial mass increased with mitochondria mostly depolarized in 8D-HYPOx compared to 8D-NORMox, with increased expression of mitochondrial genes. Proteomic and transcriptomic analyses of 8D-HYPOx revealed that the number of secreted proteins and transcripts detected also decreased compared to 8D-NORMOx and STAT, and the proteome, secretome and transcriptome harbored specific profiles that are engaged as soon as four days of incubation. Importantly, acetyl-CoA and the fatty acid pathway involving mitochondria are required for the generation and viability maintenance of VBNC. Altogether, these data show that we were able to generate for the first time VBNC phenotype in C. neoformans. This VBNC state is associated with a specific metabolism that should be further studied to understand dormancy/quiescence in this yeast.
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Affiliation(s)
- Benjamin Hommel
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Stevenn Volant
- Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | | | - Magalie Duchateau
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - Chen-Hsin Yu
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Véronique Hourdel
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - Hugo Varet
- Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
- Institut Pasteur - Transcriptome and Epigenome Platform - Biomics Pole - C2RT, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - John R. Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Françoise Dromer
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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Cereija TB, Alarico S, Lourenço EC, Manso JA, Ventura MR, Empadinhas N, Macedo-Ribeiro S, Pereira PJB. The structural characterization of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation. IUCRJ 2019; 6:572-585. [PMID: 31316802 PMCID: PMC6608630 DOI: 10.1107/s2052252519005372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/18/2019] [Indexed: 06/10/2023]
Abstract
Bacteria are challenged to adapt to environmental variations in order to survive. Under nutritional stress, several bacteria are able to slow down their metabolism into a nonreplicating state and wait for favourable conditions. It is almost universal that bacteria accumulate carbon stores to survive during this nonreplicating state and to fuel rapid proliferation when the growth-limiting stress disappears. Mycobacteria are exceedingly successful in their ability to become dormant under harsh circumstances and to be able to resume growth when conditions are favourable. Rapidly growing mycobacteria accumulate glucosylglycerate under nitrogen-limiting conditions and quickly mobilize it when nitrogen availability is restored. The depletion of intracellular glucosyl-glycerate levels in Mycolicibacterium hassiacum (basonym Mycobacterium hassiacum) was associated with the up-regulation of the gene coding for glucosylglycerate hydrolase (GgH), an enzyme that is able to hydrolyse glucosylglycerate to glycerate and glucose, a source of readily available energy. Highly conserved among unrelated phyla, GgH is likely to be involved in bacterial reactivation following nitrogen starvation, which in addition to other factors driving mycobacterial recovery may also provide an opportunity for therapeutic intervention, especially in the serious infections caused by some emerging opportunistic pathogens of this group, such as Mycobacteroides abscessus (basonym Mycobacterium abscessus). Using a combination of biochemical methods and hybrid structural approaches, the oligomeric organization of M. hassiacum GgH was determined and molecular determinants of its substrate binding and specificity were unveiled.
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Affiliation(s)
- Tatiana Barros Cereija
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Susana Alarico
- CNC – Centro de Neurociências e Biologia Celular, Universidade de Coimbra, Coimbra, Portugal
- IIIUC – Instituto de Investigação Interdisciplinar, Universidade de Coimbra, Coimbra, Portugal
| | - Eva C. Lourenço
- ITQB – Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José António Manso
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - M. Rita Ventura
- ITQB – Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Nuno Empadinhas
- CNC – Centro de Neurociências e Biologia Celular, Universidade de Coimbra, Coimbra, Portugal
- IIIUC – Instituto de Investigação Interdisciplinar, Universidade de Coimbra, Coimbra, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Pedro José Barbosa Pereira
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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Batyrshina YR, Schwartz YS. Modeling of Mycobacterium tuberculosis dormancy in bacterial cultures. Tuberculosis (Edinb) 2019; 117:7-17. [DOI: 10.1016/j.tube.2019.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/18/2019] [Accepted: 05/22/2019] [Indexed: 10/26/2022]
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124
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Mashabela GT, de Wet TJ, Warner DF. Mycobacterium tuberculosis Metabolism. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0067-2019. [PMID: 31350832 PMCID: PMC10957194 DOI: 10.1128/microbiolspec.gpp3-0067-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Indexed: 02/06/2023] Open
Abstract
Mycobacterium tuberculosis is the cause of tuberculosis (TB), a disease which continues to overwhelm health systems in endemic regions despite the existence of effective combination chemotherapy and the widespread use of a neonatal anti-TB vaccine. For a professional pathogen, M. tuberculosis retains a surprisingly large proportion of the metabolic repertoire found in nonpathogenic mycobacteria with very different lifestyles. Moreover, evidence that additional functions were acquired during the early evolution of the M. tuberculosis complex suggests the organism has adapted (and augmented) the metabolic pathways of its environmental ancestor to persistence and propagation within its obligate human host. A better understanding of M. tuberculosis pathogenicity, however, requires the elucidation of metabolic functions under disease-relevant conditions, a challenge complicated by limited knowledge of the microenvironments occupied and nutrients accessed by bacilli during host infection, as well as the reliance in experimental mycobacteriology on a restricted number of experimental models with variable relevance to clinical disease. Here, we consider M. tuberculosis metabolism within the framework of an intimate host-pathogen coevolution. Focusing on recent advances in our understanding of mycobacterial metabolic function, we highlight unusual adaptations or departures from the better-characterized model intracellular pathogens. We also discuss the impact of these mycobacterial "innovations" on the susceptibility of M. tuberculosis to existing and experimental anti-TB drugs, as well as strategies for targeting metabolic pathways. Finally, we offer some perspectives on the key gaps in the current knowledge of fundamental mycobacterial metabolism and the lessons which might be learned from other systems.
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Affiliation(s)
- Gabriel T Mashabela
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
- Current address: Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, University of Stellenbosch, South Africa
| | - Timothy J de Wet
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
- Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
- Wellcome Centre for Infectious Disease Research in Africa, University of Cape Town, South Africa
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125
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Luo D, Chen J, Xie G, Yue L, Wang Y. Enzyme characterization and biological activities of a resuscitation promoting factor from an oil degrading bacterium Rhodococcus erythropolis KB1. PeerJ 2019; 7:e6951. [PMID: 31149404 PMCID: PMC6534110 DOI: 10.7717/peerj.6951] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 04/14/2019] [Indexed: 01/28/2023] Open
Abstract
Resuscitation-promoting factors (Rpf) are a class of muralytic enzymes, which participate in recovery of dormant cells and promoting bacteria growth in poor media. In the present study the expression vector of the rpf-1 gene from an oil-degrading bacterium Rhodococcus erythropolis KB1 was constructed and expressed in Escherichia coli. The expressed protein was purified by Ni2+-affinity chromatography, and showed muralytic activity when measured with 4-methylumbelliferyl-β-D-N,N',N″-triacetyl chitotrioside as substrate. Addition of purified Rpf-1 to R. erythropolis culture efficiently improved bacterial cell growth. The purified protein also increased resuscitation of viable but nonculturable cells of R. erythropolis to culturable state. The conserved amino acid residues including Asp45, Glu51, Cys50, Thr60, Gln69, Thr74, Trp75 and Cys114 of the Rpf-1 were replaced with different amino acids. The mutant proteins were also expressed and purified with Ni2+-affinity chromatography. The muralytic activities of the mutant proteins decreased to different extents when compared with that of the wild type Rpf-1. Gln69 was found to play the most important role in the enzyme activity, substitution of Gln69 with lysine (Q69K) resulted in the greatest decrease of muralytic activity. The other amino acid residues such as Asp45, Glu51, Cys50 and Cys114 were also found to be very important in maintaining muralytic activity and biological function of the Rpf-1. Our results indicated that Rpf-1 from R. erythropolis showed muralytic activities and weak protease activity, but the muralytic activity was responsible for its growth promotion and resuscitation activity.
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Affiliation(s)
- Dan Luo
- School of Petrochemical Engineering, Lanzhou University of Technology, Lan Zhou, China
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lan Zhou, China
| | - Gang Xie
- School of Petrochemical Engineering, Lanzhou University of Technology, Lan Zhou, China
| | - Liang Yue
- School of Petrochemical Engineering, Lanzhou University of Technology, Lan Zhou, China
| | - Yonggang Wang
- School of Life science and Engineering, Lanzhou University of Technology, Lan Zhou, China
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126
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Mohammad K, Dakik P, Medkour Y, Mitrofanova D, Titorenko VI. Quiescence Entry, Maintenance, and Exit in Adult Stem Cells. Int J Mol Sci 2019; 20:ijms20092158. [PMID: 31052375 PMCID: PMC6539837 DOI: 10.3390/ijms20092158] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/24/2019] [Accepted: 04/28/2019] [Indexed: 12/13/2022] Open
Abstract
Cells of unicellular and multicellular eukaryotes can respond to certain environmental cues by arresting the cell cycle and entering a reversible state of quiescence. Quiescent cells do not divide, but can re-enter the cell cycle and resume proliferation if exposed to some signals from the environment. Quiescent cells in mammals and humans include adult stem cells. These cells exhibit improved stress resistance and enhanced survival ability. In response to certain extrinsic signals, adult stem cells can self-renew by dividing asymmetrically. Such asymmetric divisions not only allow the maintenance of a population of quiescent cells, but also yield daughter progenitor cells. A multistep process of the controlled proliferation of these progenitor cells leads to the formation of one or more types of fully differentiated cells. An age-related decline in the ability of adult stem cells to balance quiescence maintenance and regulated proliferation has been implicated in many aging-associated diseases. In this review, we describe many traits shared by different types of quiescent adult stem cells. We discuss how these traits contribute to the quiescence, self-renewal, and proliferation of adult stem cells. We examine the cell-intrinsic mechanisms that allow establishing and sustaining the characteristic traits of adult stem cells, thereby regulating quiescence entry, maintenance, and exit.
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Affiliation(s)
- Karamat Mohammad
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Paméla Dakik
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Younes Medkour
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Darya Mitrofanova
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
| | - Vladimir I Titorenko
- Department of Biology, Concordia University, 7141 Sherbrooke Street, West, SP Building, Room 501-13, Montreal, QC H4B 1R6, Canada.
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127
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Jackson SA, Schoeni JL, Vegge C, Pane M, Stahl B, Bradley M, Goldman VS, Burguière P, Atwater JB, Sanders ME. Improving End-User Trust in the Quality of Commercial Probiotic Products. Front Microbiol 2019; 10:739. [PMID: 31105649 PMCID: PMC6499161 DOI: 10.3389/fmicb.2019.00739] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/25/2019] [Indexed: 01/09/2023] Open
Abstract
In a rapidly growing global probiotic market, end-users have difficulty distinguishing between high quality and poor quality products. This ambiguity threatens the trust consumers and healthcare providers have in probiotic products. To address this problem, we recommend that companies undergo third-party evaluations to certify probiotic quality and label accuracy. In order to communicate about product quality to end-users, indication of certification on product labels is helpful, although not all manufacturers choose to use this approach. Herein we discuss: third-party certification, the process of setting standards for identity, purity, and quantification of probiotics; some emerging methodologies useful for quality assessment; and some technical challenges unique to managing quality of live microbial products. This review provides insights of an Expert Panel engaged in this process and aims to update the reader on relevant current scientific methodologies. Establishing validated methodologies for all aspects of quality assessment is an essential component of this process and can be facilitated by established organizations, such as United States Pharmacopeia. Emerging methodologies including whole genome sequencing and flow cytometry are poised to play important roles in these processes.
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Affiliation(s)
- Scott A. Jackson
- National Institute of Standards and Technology, Gaithersburg, MD, United States
| | - Jean L. Schoeni
- Eurofins Food Integrity and Innovation, Madison, WI, United States
| | | | | | - Buffy Stahl
- DuPont Nutrition & Health, Madison, WI, United States
| | | | - Virginia S. Goldman
- Department of Dietary Supplements and Herbal Medicines, Science Division, US Pharmacopeial Convention, Rockville, MD, United States
| | | | | | - Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Sacramento, CA, United States
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128
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Bravo Z, Orruño M, Navascues T, Ogayar E, Ramos-Vivas J, Kaberdin VR, Arana I. Analysis of Acinetobacter baumannii survival in liquid media and on solid matrices as well as effect of disinfectants. J Hosp Infect 2019; 103:e42-e52. [PMID: 30986481 DOI: 10.1016/j.jhin.2019.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/07/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Acinetobacter baumannii is a cause of healthcare-associated infections and has considerable potential to survive on inanimate hospital surfaces under hostile conditions (e.g. disinfection or desiccation). AIM To learn more about its survival strategy and capacity to persist in liquid media and on surfaces mimicking hospital environments. METHODS The effect of temperature, nutrient deprivation, permanence on inanimate surfaces, and exposure to disinfectants on the survival of four A. baumannii strains (ATCC 19606T and three clinical isolates) was studied by monitoring the number of total and viable cells using fluorescent microscopy and of culturable cells by standard cultures. FINDINGS Bacterial survival was differentially affected by temperature (cells maintained at 20°C remained culturable at least within 30 days) and physical environment (desiccation favoured cell resistance to stress at 37°C). Moreover, persistence was associated with two adaptation patterns: one linked to entry into the viable but non-culturable state, whereas the other apparently followed a bust-and-boom model. During a study on the effect of disinfectant (commercial bleach and quaternary ammonium compounds), it was found that treatment with these antibacterial compounds did not eliminate A. baumannii populations and provoked the reduction of culturable populations, although a fraction of cells remained culturable. CONCLUSION The ability to persist for long periods on different surfaces, mimicking those usually found in hospitals, along with A. baumannii's capacity to survive after a disinfection process may account for the recurrent outbreaks in intensive care units.
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Affiliation(s)
- Z Bravo
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain; Instituto de Investigación Valdecilla IDIVAL, Santander, Spain
| | - M Orruño
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), Plentzia, Spain.
| | - T Navascues
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain; Instituto de Investigación Valdecilla IDIVAL, Santander, Spain
| | - E Ogayar
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - J Ramos-Vivas
- Instituto de Investigación Valdecilla IDIVAL, Santander, Spain
| | - V R Kaberdin
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), Plentzia, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - I Arana
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE-UPV/EHU), Plentzia, Spain
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129
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Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota. Proc Natl Acad Sci U S A 2019; 116:8499-8504. [PMID: 30975748 PMCID: PMC6486781 DOI: 10.1073/pnas.1820594116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is well-understood that many bacteria have evolved to survive catastrophic events using a variety of mechanisms, which include expression of stress-response genes, quiescence, necrotrophy, and metabolic advantages obtained through mutation. However, the dynamics of individuals leveraging these abilities to gain a competitive advantage in an ecologically complex setting remain unstudied. In this study, we observed the saliva microbiome throughout the ecological perturbation of long-term starvation, allowing only the species best equipped to access and use the limited resources to survive. During the first several days, the community underwent a death phase that resulted in a ∼50-100-fold reduction in the number of viable cells. Interestingly, after this death phase, only three species, Klebsiella pneumoniae, Klebsiella oxytoca, and Providencia alcalifaciens, all members of the family Enterobacteriaceae, appeared to be transcriptionally active and recoverable. Klebsiella are significant human pathogens, frequently resistant to multiple antibiotics, and recently, ectopic colonization of the gut by oral Klebsiella was documented to induce dysbiosis and inflammation. MetaOmics analyses provided several leads for further investigation regarding the ecological success of the Enterobacteriaceae. The isolates accumulated single nucleotide polymorphisms in known growth advantage in stationary phase alleles and produced natural products closely resembling antimicrobial cyclic depsipeptides. The results presented in this study suggest that pathogenic Enterobacteriaceae persist much longer than their more benign neighbors in the salivary microbiome when faced with starvation. This is particularly significant, given that hospital surfaces contaminated with oral fluids, especially sinks and drains, are well-established sources of outbreaks of drug-resistant Enterobacteriaceae.
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130
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Saelens JW, Viswanathan G, Tobin DM. Mycobacterial Evolution Intersects With Host Tolerance. Front Immunol 2019; 10:528. [PMID: 30967867 PMCID: PMC6438904 DOI: 10.3389/fimmu.2019.00528] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Over the past 200 years, tuberculosis (TB) has caused more deaths than any other infectious disease, likely infecting more people than it has at any other time in human history. Mycobacterium tuberculosis (Mtb), the etiologic agent of TB, is an obligate human pathogen that has evolved through the millennia to become an archetypal human-adapted pathogen. This review focuses on the evolutionary framework by which Mtb emerged as a specialized human pathogen and applies this perspective to the emergence of specific lineages that drive global TB burden. We consider how evolutionary pressures, including transmission dynamics, host tolerance, and human population patterns, may have shaped the evolution of diverse mycobacterial genomes.
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Affiliation(s)
- Joseph W. Saelens
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Gopinath Viswanathan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - David M. Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
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131
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Minasyan H. Sepsis: mechanisms of bacterial injury to the patient. Scand J Trauma Resusc Emerg Med 2019; 27:19. [PMID: 30764843 PMCID: PMC6376788 DOI: 10.1186/s13049-019-0596-4] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/01/2019] [Indexed: 12/17/2022] Open
Abstract
In bacteremia the majority of bacterial species are killed by oxidation on the surface of erythrocytes and digested by local phagocytes in the liver and the spleen. Sepsis-causing bacteria overcome this mechanism of human innate immunity by versatile respiration, production of antioxidant enzymes, hemolysins, exo- and endotoxins, exopolymers and other factors that suppress host defense and provide bacterial survival. Entering the bloodstream in different forms (planktonic, encapsulated, L-form, biofilm fragments), they cause different types of sepsis (fulminant, acute, subacute, chronic, etc.). Sepsis treatment includes antibacterial therapy, support of host vital functions and restore of homeostasis. A bacterium killing is only one of numerous aspects of antibacterial therapy. The latter should inhibit the production of bacterial antioxidant enzymes and hemolysins, neutralize bacterial toxins, modulate bacterial respiration, increase host tolerance to bacterial products, facilitate host bactericidal mechanism and disperse bacterial capsule and biofilm.
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132
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Wong J, Choi SYC, Liu R, Xu E, Killam J, Gout PW, Wang Y. Potential Therapies for Infectious Diseases Based on Targeting Immune Evasion Mechanisms That Pathogens Have in Common With Cancer Cells. Front Cell Infect Microbiol 2019; 9:25. [PMID: 30809511 PMCID: PMC6379255 DOI: 10.3389/fcimb.2019.00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/24/2019] [Indexed: 12/18/2022] Open
Abstract
Many global infectious diseases are not well-controlled, underlining a critical need for new, more effective therapies. Pathogens and pathogen-infected host cells, like cancer cells, evade immune surveillance via immune evasion mechanisms. The present study indicates that pathogenic bacteria, endoparasites, and virus-infected host cells can have immune evasion mechanisms in common with cancers. These include entry into dormancy and metabolic reprogramming to aerobic glycolysis leading to excessive secretion of lactic acid and immobilization of local host immunity. The latter evasion tactic provides a therapeutic target for cancer, as shown by our recent finding that patient-derived cancer xenografts can be growth-arrested, without major host toxicity, by inhibiting their lactic acid secretion (as mediated by the MCT4 transporter)-with evidence of host immunity restoration. Accordingly, the multiplication of bacteria, endoparasites, and viruses that primarily depend on metabolic reprogramming to aerobic glycolysis for survival may be arrested using cancer treatment strategies that inhibit their lactic acid secretion. Immune evasion mechanisms shared by pathogens and cancer cells likely represent fundamental, evolutionarily-conserved mechanisms that may be particularly critical to their welfare. As such, their targeting may lead to novel therapies for infectious diseases.
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Affiliation(s)
- Jodi Wong
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Stephen Yiu Chuen Choi
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada.,Vancouver Prostate Centre, Vancouver, BC, Canada.,Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Rongrong Liu
- Department of Microbiology, School of Basic Medicine, Fourth Military Medical University, Xi'an, China
| | - Eddie Xu
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada.,Vancouver Prostate Centre, Vancouver, BC, Canada.,Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - James Killam
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Peter W Gout
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Yuzhuo Wang
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada.,Vancouver Prostate Centre, Vancouver, BC, Canada.,Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
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133
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Sagot I, Laporte D. Quiescence, an individual journey. Curr Genet 2019; 65:695-699. [PMID: 30649583 DOI: 10.1007/s00294-018-00928-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 12/14/2022]
Abstract
Quiescence is operationally characterized as a temporary and reversible proliferation arrest. There are many preconceived ideas about quiescence, quiescent cells being generally viewed as insignificant sleeping G1 cells. In fact, quiescence is central for organism physiology and its dysregulation involved in many pathologies. The quiescent state encompasses very diverse cellular situations depending on the cell type and its environment. This diversity challenges not only quiescence uniformity but also the universality of the molecular mechanisms beyond quiescence regulation. In this mini-perspective, we discuss recent advances in the concept of quiescence, and illustrate that this multifaceted cellular state is gaining increasing attention in many fields of biology.
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Affiliation(s)
- Isabelle Sagot
- Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, Unité Mixte de Recherche 5095, Université de Bordeaux, CS61390, Bordeaux Cedex, 33077, France.
| | - Damien Laporte
- Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, Unité Mixte de Recherche 5095, Université de Bordeaux, CS61390, Bordeaux Cedex, 33077, France
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134
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Sagot I, Laporte D. The cell biology of quiescent yeast – a diversity of individual scenarios. J Cell Sci 2019; 132:132/1/jcs213025. [DOI: 10.1242/jcs.213025] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
ABSTRACT
Most cells, from unicellular to complex organisms, spend part of their life in quiescence, a temporary non-proliferating state. Although central for a variety of essential processes including tissue homeostasis, development and aging, quiescence is poorly understood. In fact, quiescence encompasses various cellular situations depending on the cell type and the environmental niche. Quiescent cell properties also evolve with time, adding another layer of complexity. Studying quiescence is, above all, limited by the fact that a quiescent cell can be recognized as such only after having proved that it is capable of re-proliferating. Recent cellular biology studies in yeast have reported the relocalization of hundreds of proteins and the reorganization of several cellular machineries upon proliferation cessation. These works have revealed that quiescent cells can display various properties, shedding light on a plethora of individual behaviors. The deciphering of the molecular mechanisms beyond these reorganizations, together with the understanding of their cellular functions, have begun to provide insights into the physiology of quiescent cells. In this Review, we discuss recent findings and emerging concepts in Saccharomyces cerevisiae quiescent cell biology.
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Affiliation(s)
- Isabelle Sagot
- Centre National de la Recherche Scientifique, Université de Bordeaux-Institut de Biochimie et Génétique Cellulaires, UMR5095-33077 Bordeaux cedex, France
| | - Damien Laporte
- Centre National de la Recherche Scientifique, Université de Bordeaux-Institut de Biochimie et Génétique Cellulaires, UMR5095-33077 Bordeaux cedex, France
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135
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Takeuchi T, Benning C. Nitrogen-dependent coordination of cell cycle, quiescence and TAG accumulation in Chlamydomonas. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:292. [PMID: 31890020 PMCID: PMC6927116 DOI: 10.1186/s13068-019-1635-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/12/2019] [Indexed: 05/07/2023]
Abstract
Microalgae hold great promises as sustainable cellular factories for the production of alternative fuels, feeds, and biopharmaceuticals for human health. While the biorefinery approach for fuels along with the coproduction of high-value compounds with industrial, therapeutic, or nutraceutical applications have the potential to make algal biofuels more economically viable, a number of challenges continue to hamper algal production systems at all levels. One such hurdle includes the metabolic trade-off often observed between the increased yields of desired products, such as triacylglycerols (TAG), and the growth of an organism. Initial genetic engineering strategies to improve lipid productivity in microalgae, which focused on overproducing the enzymes involved in fatty acid and TAG biosynthesis or inactivating competing carbon (C) metabolism, have seen some successes albeit at the cost of often greatly reduced biomass. Emergent approaches that aim at modifying the dynamics of entire metabolic pathways by engineering of pertinent transcription factors or signaling networks appear to have successfully achieved a balance between growth and neutral lipid accumulation. However, the biological knowledge of key signaling networks and molecular components linking these two processes is still incomplete in photosynthetic eukaryotes, making it difficult to optimize metabolic engineering strategies for microalgae. Here, we focus on nitrogen (N) starvation of the model green microalga, Chlamydomonas reinhardtii, to present the current understanding of the nutrient-dependent switch between proliferation and quiescence, and the drastic reprogramming of metabolism that results in the storage of C compounds following N starvation. We discuss the potential components mediating the transcriptional repression of cell cycle genes and the establishment of quiescence in Chlamydomonas, and highlight the importance of signaling pathways such as those governed by the target of rapamycin (TOR) and sucrose nonfermenting-related (SnRK) kinases in the coordination of metabolic status with cellular growth. A better understanding of how the cell division cycle is regulated in response to nutrient scarcity and of the signaling pathways linking cellular growth to energy and lipid homeostasis, is essential to improve the prospects of biofuels and biomass production in microalgae.
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Affiliation(s)
- Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
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136
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Bertschi NL, Voorberg-van der Wel A, Zeeman AM, Schuierer S, Nigsch F, Carbone W, Knehr J, Gupta DK, Hofman SO, van der Werff N, Nieuwenhuis I, Klooster E, Faber BW, Flannery EL, Mikolajczak SA, Chuenchob V, Shrestha B, Beibel M, Bouwmeester T, Kangwanrangsan N, Sattabongkot J, Diagana TT, Kocken CH, Roma G. Transcriptomic analysis reveals reduced transcriptional activity in the malaria parasite Plasmodium cynomolgi during progression into dormancy. eLife 2018; 7:41081. [PMID: 30589413 PMCID: PMC6344078 DOI: 10.7554/elife.41081] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/23/2018] [Indexed: 02/06/2023] Open
Abstract
Relapses of Plasmodium dormant liver hypnozoites compromise malaria eradication efforts. New radical cure drugs are urgently needed, yet the vast gap in knowledge of hypnozoite biology impedes drug discovery. We previously unraveled the transcriptome of 6 to 7 day-old P. cynomolgi liver stages, highlighting pathways associated with hypnozoite dormancy (Voorberg-van der Wel et al., 2017). We now extend these findings by transcriptome profiling of 9 to 10 day-old liver stage parasites, thus revealing for the first time the maturation of the dormant stage over time. Although progression of dormancy leads to a 10-fold decrease in transcription and expression of only 840 genes, including genes associated with housekeeping functions, we show that pathways involved in quiescence, energy metabolism and maintenance of genome integrity remain the prevalent pathways active in mature hypnozoites.
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Affiliation(s)
- Nicole L Bertschi
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | | | - Anne-Marie Zeeman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Florian Nigsch
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Judith Knehr
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Devendra K Gupta
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | - Sam O Hofman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Nicole van der Werff
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ivonne Nieuwenhuis
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Els Klooster
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Bart W Faber
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Erika L Flannery
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | | | - Vorada Chuenchob
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | - Binesh Shrestha
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Martin Beibel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Niwat Kangwanrangsan
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thierry T Diagana
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | - Clemens Hm Kocken
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
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137
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Matallana-Surget S, Werner J, Wattiez R, Lebaron K, Intertaglia L, Regan C, Morris J, Teeling H, Ferrer M, Golyshin PN, Gerogiorgis D, Reilly SI, Lebaron P. Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean. Front Microbiol 2018; 9:3125. [PMID: 30622520 PMCID: PMC6308992 DOI: 10.3389/fmicb.2018.03125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/03/2018] [Indexed: 12/16/2022] Open
Abstract
Epibacterium mobile BBCC367 is a marine bacterium that is common in coastal areas. It belongs to the Roseobacter clade, a widespread group in pelagic marine ecosystems. Species of the Roseobacter clade are regularly used as models to understand the evolution and physiological adaptability of generalist bacteria. E. mobile BBCC367 comprises two chromosomes and two plasmids. We used gel-free shotgun proteomics to assess its protein expression under 16 different conditions, including stress factors such as elevated temperature, nutrient limitation, high metal concentration, and UVB exposure. Comparison of the different conditions allowed us not only to retrieve almost 70% of the predicted proteins, but also to define three main protein assemblages: 584 essential core proteins, 2,144 facultative accessory proteins and 355 specific unique proteins. While the core proteome mainly exhibited proteins involved in essential functions to sustain life such as DNA, amino acids, carbohydrates, cofactors, vitamins and lipids metabolisms, the accessory and unique proteomes revealed a more specific adaptation with the expression of stress-related proteins, such as DNA repair proteins (accessory proteome), transcription regulators and a significant predominance of transporters (unique proteome). Our study provides insights into how E. mobile BBCC367 adapts to environmental changes and copes with diverse stresses.
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Affiliation(s)
- Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, Rostock, Germany
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Interdisciplinary Mass Spectrometry Center (CISMa), University of Mons, Mons, Belgium
| | - Karine Lebaron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Laurent Intertaglia
- Sorbonne Universites, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls/Mer, France.,Sorbonne Universites, UPMC Univ Paris 06, CNRS, Observatoire Océanologique de Banyuls (OOB), Banyuls/Mer, France
| | - Callum Regan
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - James Morris
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Hanno Teeling
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Manuel Ferrer
- Department of Applied Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain
| | - Peter N Golyshin
- School of Natural Sciences, University of Bangor, Bangor, United Kingdom
| | - Dimitrios Gerogiorgis
- Institute for Materials and Processes, School of Engineering, University of Edinburgh, The King's Buildings, Edinburgh, United Kingdom
| | - Simon I Reilly
- School of Natural Sciences, University of Bangor, Bangor, United Kingdom
| | - Philippe Lebaron
- Sorbonne Universites, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls/Mer, France.,Sorbonne Universites, UPMC Univ Paris 06, CNRS, Observatoire Océanologique de Banyuls (OOB), Banyuls/Mer, France
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138
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Porcar M, Louie KB, Kosina SM, Van Goethem MW, Bowen BP, Tanner K, Northen TR. Microbial Ecology on Solar Panels in Berkeley, CA, United States. Front Microbiol 2018; 9:3043. [PMID: 30619134 PMCID: PMC6297676 DOI: 10.3389/fmicb.2018.03043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/26/2018] [Indexed: 11/13/2022] Open
Abstract
Solar panels can be found practically all over the world and represent a standard surface that can be colonized by microbial communities that are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations and desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also standard devices to study the microbial communities and their colonization process from different areas of Earth. We report here a comprehensive description of the microbial communities associated with solar panels in Berkeley, CA, United States. Cultivable bacteria were isolated to characterize their adhesive capabilities, and UV- and desiccation-resistance properties. Furthermore, a parallel culture-independent metagenomic and metabolomic approach has allowed us to gain insight on the taxonomic and functional nature of these communities. Metagenomic analysis was performed using the Illumina HiSeq2500 sequencing platform, revealing that the bacterial population of the Berkeley solar panels is composed mainly of Actinobacteria, Bacteroidetes and Proteobacteria, as well as lower amounts of Deinococcus-Thermus and Firmicutes. Furthermore, a clear predominance of Hymenobacter sp. was also observed. A functional analysis revealed that pathways involved in the persistence of microbes on solar panels (i.e., stress response, capsule development, and metabolite repair) and genes assigned to carotenoid biosynthesis were common to all metagenomes. On the other hand, genes involved in photosynthetic pathways and general autotrophic subsystems were rare, suggesting that these pathways are not critical for persistence on solar panels. Metabolomics was performed using a liquid chromatography tandem mass spectrometry (LC-MS/MS) approach. When comparing the metabolome of the solar panels from Berkeley and from Valencia (Spain), a very similar composition in polar metabolites could be observed, although some metabolites appeared to be differentially represented (for example, trigonelline, pantolactone and 5-valerolactone were more abundant in the samples from Valencia than in the ones from Berkeley). Furthermore, triglyceride metabolites were highly abundant in all the solar panel samples, and both locations displayed similar profiles. The comparison of the taxonomic profile of the Californian solar panels with those previously described in Spain revealed striking similarities, highlighting the central role of both selective pressures and the ubiquity of microbial populations in the colonization and establishment of microbial communities.
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Affiliation(s)
- Manuel Porcar
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Paterna, Spain.,Darwin Bioprospecting Excellence S.L., Parc Científic de la Universitat de València, Paterna, Spain.,Lawrence Berkeley National Laboratory, Joint Genome Institute, Walnut Creek, CA, United States
| | - Katherine B Louie
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Walnut Creek, CA, United States
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marc W Van Goethem
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P Bowen
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Walnut Creek, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kristie Tanner
- Darwin Bioprospecting Excellence S.L., Parc Científic de la Universitat de València, Paterna, Spain
| | - Trent R Northen
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Walnut Creek, CA, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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139
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Muller KE, Denison RF. Resource acquisition and allocation traits in symbiotic rhizobia with implications for life-history outside of legume hosts. ROYAL SOCIETY OPEN SCIENCE 2018; 5:181124. [PMID: 30662731 PMCID: PMC6304121 DOI: 10.1098/rsos.181124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/13/2018] [Indexed: 05/07/2023]
Abstract
Resources that microbial symbionts obtain from hosts may enhance fitness during free-living stages when resources are comparatively scarce. For rhizobia in legume root nodules, diverting resources from nitrogen fixation to polyhydroxybutyrate (PHB) has been discussed as a source of host-symbiont conflict. Yet, little is known about natural variation in PHB storage and its implications for rhizobial evolution. We therefore measured phenotypic variation in natural rhizobia populations and investigated how PHB might contribute to fitness in the free-living stage. We found that natural populations of rhizobia from Glycine max and Chamaecrista fasciculata had substantial, heritable variation in PHB acquisition during symbiosis. A model simulating temperature-dependent metabolic activity showed that the observed range of stored PHB per cell could support survival for a few days, for active cells, or over a century for sufficiently dormant cells. Experiments with field-isolated Bradyrhizobium in starvation culture suggest PHB is partitioned asymmetrically in dividing cells, consistent with individual-level bet-hedging previously demonstrated in E. meliloti. High-PHB isolates used more PHB over the first month, yet still retained more PHB for potential long-term survival in a dormant state. These results suggest that stored resources like PHB may support both short-term and long-term functions that contribute to fitness in the free-living stage.
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Affiliation(s)
- Katherine E. Muller
- Graduate Program in Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA
| | - R. Ford Denison
- Department of Ecology Evolution and Behavior, University of Minnesota, St Paul, MN, USA
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140
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Bekale RB, Du Plessis SM, Hsu NJ, Sharma JR, Sampson SL, Jacobs M, Meyer M, Morse GD, Dube A. Mycobacterium Tuberculosis and Interactions with the Host Immune System: Opportunities for Nanoparticle Based Immunotherapeutics and Vaccines. Pharm Res 2018; 36:8. [PMID: 30411187 PMCID: PMC6362825 DOI: 10.1007/s11095-018-2528-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/17/2018] [Indexed: 02/06/2023]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis remains a deadly infectious disease. The thin pipeline of new drugs for TB, the ineffectiveness in adults of the only vaccine available, i.e. the Bacillus Calmette-Guerin vaccine, and increasing global antimicrobial resistance, has reinvigorated interest in immunotherapies. Nanoparticles (NPs) potentiate the effect of immune modulating compounds (IMC), enabling cell targeting, improved transfection of antigens, enhanced compound stability and provide opportunities for synergistic action, via delivery of multiple IMCs. In this review we describe work performed in the application of NPs towards achieving immune modulation for TB treatment and vaccination. Firstly, we present a comprehensive review of M. tuberculosis and how the bacterium modulates the host immune system. We find that current work suggest great promise of NP based immunotherapeutics as novel treatments and vaccination systems. There is need to intensify research efforts in this field, and rationally design novel NP immunotherapeutics based on current knowledge of the mycobacteriology and immune escape mechanisms employed by M. tuberculosis.
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Affiliation(s)
- Raymonde B Bekale
- Discipline of Pharmaceutics, School of Pharmacy, University of the Western Cape, Cape Town, South Africa
| | - Su-Mari Du Plessis
- NRF-DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nai-Jen Hsu
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jyoti R Sharma
- National Health Laboratory Service, Johannesburg, South Africa
| | - Samantha L Sampson
- NRF-DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Muazzam Jacobs
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Johannesburg, South Africa
- Immunology of Infectious Disease Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Mervin Meyer
- DST/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Unit, Department of Biotechnology, University of the Western Cape (UWC), Cape Town, South Africa
| | - Gene D Morse
- AIDS Clinical Trials Group Pharmacology Specialty Laboratory, New York State Center of Excellence in Bioinformatics and Life Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Admire Dube
- Discipline of Pharmaceutics, School of Pharmacy, University of the Western Cape, Cape Town, South Africa.
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141
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Low YM, Chong CW, Yap IKS, Chai LC, Clarke SC, Ponnampalavanar S, Abdul Jabar K, Md Yusof MY, Teh CSJ. Elucidating the survival and response of carbapenem resistant Klebsiella pneumoniae after exposure to imipenem at sub-lethal concentrations. Pathog Glob Health 2018; 112:378-386. [PMID: 30380366 DOI: 10.1080/20477724.2018.1538281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The increasing prevalence of antibiotic resistant pathogens poses a serious threat to global health. However, less emphasis has been placed to co-relate the gene expression and metabolism of antibiotic resistant pathogens. This study aims to elucidate gene expression and variations in metabolism of multidrug resistant Klebsiella pneumoniae after exposure to antibiotics. Phenotypic responses of three genotypically distinct carbapenem resistant Klebsiella pneumoniae (CRKP) strains untreated and treated with sub-lethal concentrations of imipenem were investigated via phenotype microarrays (PM). The gene expression and metabolism of the strain harboring blaNDM-1 before and after exposure to sub-lethal concentration of imipenem were further investigated by RNA-sequencing (RNA-Seq) and 1H NMR spectroscopy respectively. Most genes related to cell division, central carbon metabolism and nucleotide metabolism were downregulated after imipenem treatment. Similarly, 1H NMR spectra obtained from treated CRKP showed decrease in levels of bacterial end products (acetate, pyruvate, succinate, formate) and metabolites involved in nucleotide metabolism (uracil, xanthine, hypoxanthine) but elevated levels of glycerophosphocholine. The presence of anserine was also observed for the treated CRKP while FAPγ-adenine and methyladenine were only present in untreated bacterial cells. As a conclusion, the studied CRKP strain exhibited decrease in central carbon metabolism, cell division and nucleotide metabolism after exposure to sub-lethal concentrations of imipenem. The understanding of the complex biological system of this multidrug resistant bacterium may help in the development of novel strategies and potential targets for the management of the infections.
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Affiliation(s)
- Ye Mun Low
- a Department of Medical Microbiology, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
| | - Chun Wie Chong
- b Department of Life Sciences, School of Pharmacy , International Medical University , Bukit Jalil , Kuala Lumpur , Malaysia.,c Centre for Translational Research, Institute for Research, Development and Innovation , International Medical University , Kuala Lumpur , Malaysia
| | - Ivan Kok Seng Yap
- d Clinical Research Centre, Sarawak General Hospital , Jalan Hospital , Kuching , Malaysia
| | - Lay Ching Chai
- e Institute of Biological Sciences , University of Malaya , Kuala Lumpur , Malaysia
| | - Stuart C Clarke
- f Faculty of Medicine and Institute for Life Sciences and Global Health Research Institute , University of Southampton , Southampton , UK.,g NIHR Southampton Biomedical Research Centre , Southampton , UK.,h School of Postgraduate Studies , International Medical University , Kuala Lumpur , Malaysia
| | | | - Kartini Abdul Jabar
- a Department of Medical Microbiology, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
| | - Mohd Yasim Md Yusof
- a Department of Medical Microbiology, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
| | - Cindy Shuan Ju Teh
- a Department of Medical Microbiology, Faculty of Medicine , University of Malaya , Kuala Lumpur , Malaysia
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142
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Walton EM, Cronan MR, Cambier CJ, Rossi A, Marass M, Foglia MD, Brewer WJ, Poss KD, Stainier DYR, Bertozzi CR, Tobin DM. Cyclopropane Modification of Trehalose Dimycolate Drives Granuloma Angiogenesis and Mycobacterial Growth through Vegf Signaling. Cell Host Microbe 2018; 24:514-525.e6. [PMID: 30308157 PMCID: PMC6201760 DOI: 10.1016/j.chom.2018.09.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/06/2018] [Accepted: 09/06/2018] [Indexed: 01/22/2023]
Abstract
Mycobacterial infection leads to the formation of characteristic immune aggregates called granulomas, a process accompanied by dramatic remodeling of the host vasculature. As granuloma angiogenesis favors the infecting mycobacteria, it may be actively promoted by bacterial determinants during infection. Using Mycobacterium marinum-infected zebrafish as a model, we identify the enzyme proximal cyclopropane synthase of alpha-mycolates (PcaA) as an important bacterial determinant of granuloma-associated angiogenesis. cis-Cyclopropanation of mycobacterial mycolic acids by pcaA drives the activation of host Vegf signaling within granuloma macrophages. Cyclopropanation of the mycobacterial cell wall glycolipid trehalose dimycolate is both required and sufficient to induce robust host angiogenesis. Inducible genetic inhibition of angiogenesis and Vegf signaling during granuloma formation results in bacterial growth deficits. Together, these data reveal a mechanism by which PcaA-mediated cis-cyclopropanation of mycolic acids promotes bacterial growth and dissemination in vivo by eliciting granuloma vascularization and suggest potential approaches for host-directed therapies.
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Affiliation(s)
- Eric M Walton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark R Cronan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - C J Cambier
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Andrea Rossi
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Michele Marass
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Matthew D Foglia
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA; Regeneration Next, Duke University, Durham, NC 27710, USA
| | - W Jared Brewer
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth D Poss
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA; Regeneration Next, Duke University, Durham, NC 27710, USA
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - David M Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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143
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Superoxide dismutase activity confers (p)ppGpp-mediated antibiotic tolerance to stationary-phase Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2018; 115:9797-9802. [PMID: 30201715 PMCID: PMC6166797 DOI: 10.1073/pnas.1804525115] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metabolically quiescent bacteria represent a large proportion of those in natural and host environments, and they are often refractory to antibiotic treatment. Such drug tolerance is also observed in the laboratory during stationary phase, when bacteria face stress and starvation-induced growth arrest. Tolerance requires (p)ppGpp signaling, which mediates the stress and starvation stringent response (SR), but the downstream effectors that confer tolerance are unclear. We previously demonstrated that the SR is linked to increased antioxidant defenses in Pseudomonas aeruginosa We now demonstrate that superoxide dismutase (SOD) activity is a key factor in SR-mediated multidrug tolerance in stationary-phase P. aeruginosa Inactivation of the SR leads to loss of SOD activity and decreased multidrug tolerance during stationary phase. Genetic or chemical complementation of SOD activity of the ΔrelA spoT mutant (ΔSR) is sufficient to restore antibiotic tolerance to WT levels. Remarkably, we observe high membrane permeability and increased drug internalization upon ablation of SOD activity. Combined, our results highlight an unprecedented mode of SR-mediated multidrug tolerance in stationary-phase P. aeruginosa and suggest that inhibition of SOD activity may potentiate current antibiotics.
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144
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Scutigliani EM, Scholl ER, Grootemaat AE, Khanal S, Kochan JA, Krawczyk PM, Reits EA, Garzan A, Ngo HX, Green KD, Garneau-Tsodikova S, Ruijter JM, van Veen HA, van der Wel NN. Interfering With DNA Decondensation as a Strategy Against Mycobacteria. Front Microbiol 2018; 9:2034. [PMID: 30233521 PMCID: PMC6135046 DOI: 10.3389/fmicb.2018.02034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis is once again a major global threat, leading to more than 1 million deaths each year. Treatment options for tuberculosis patients are limited, expensive and characterized by severe side effects, especially in the case of multidrug-resistant forms. Uncovering novel vulnerabilities of the pathogen is crucial to generate new therapeutic strategies. Using high resolution microscopy techniques, we discovered one such vulnerability of Mycobacterium tuberculosis. We demonstrate that the DNA of M. tuberculosis can condense under stressful conditions such as starvation and antibiotic treatment. The DNA condensation is reversible and specific for viable bacteria. Based on these observations, we hypothesized that blocking the recovery from the condensed state could weaken the bacteria. We showed that after inducing DNA condensation, and subsequent blocking of acetylation of DNA binding proteins, the DNA localization in the bacteria is altered. Importantly under these conditions, Mycobacterium smegmatis did not replicate and its survival was significantly reduced. Our work demonstrates that agents that block recovery from the condensed state of the nucleoid can be exploited as antibiotic. The combination of fusidic acid and inhibition of acetylation of DNA binding proteins, via the Eis enzyme, potentiate the efficacy of fusidic acid by 10 and the Eis inhibitor to 1,000-fold. Hence, we propose that successive treatment with antibiotics and drugs interfering with recovery from DNA condensation constitutes a novel approach for treatment of tuberculosis and related bacterial infections.
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Affiliation(s)
- Enzo M Scutigliani
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Edwin R Scholl
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Anita E Grootemaat
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Sadhana Khanal
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Jakub A Kochan
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | | | - Eric A Reits
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Atefeh Garzan
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | - Huy X Ngo
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | - Keith D Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | | | - Jan M Ruijter
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Henk A van Veen
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Nicole N van der Wel
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
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145
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Resuscitation-Promoting Factors Are Required for Mycobacterium smegmatis Biofilm Formation. Appl Environ Microbiol 2018; 84:AEM.00687-18. [PMID: 29915116 DOI: 10.1128/aem.00687-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/10/2018] [Indexed: 12/19/2022] Open
Abstract
Resuscitation-promoting factors (Rpfs) have previously been shown to act as growth-stimulatory molecules via their lysozyme-like activity on peptidoglycan in the bacterial cell wall. In this study, we investigated the ability of Mycobacterium smegmatis strains lacking rpf genes to form biofilms and tested their susceptibilities to cell wall-targeting agents. M. smegmatis contains four distinct rpf homologues, namely, MSMEG_5700 (rpfA), MSMEG_5439 (rpfB), MSMEG_4640 (rpfE2), and MSMEG_4643 (rpfE). During axenic growth of the wild-type strain, all four mRNA transcripts were expressed to various degrees, but the expression of MSMEG_4643 was significantly greater during exponential growth. Similarly, all rpf mRNA transcripts could be detected in biofilms grown for 7, 14, and 28 days, with MSMEG_4643 expressed at the highest abundance after 7 days. In-frame unmarked deletion mutants (single and combinatorial) were generated and displayed altered colony morphologies and the inability to form typical biofilms. Moreover, any strain lacking rpfA and rpfB simultaneously exhibited increased susceptibility to rifampin, vancomycin, and SDS. Exogenous Rpf supplementation in the form of culture filtrate failed to restore biofilm formation. Liquid chromatography-mass spectrometry (LC-MS) analysis of peptidoglycan (PG) suggested a reduction in 4-3 cross-linked PG in the ΔrpfABEE2 mutant strain. In addition, the level of PG-repeat units terminating in 1,6-anhydroMurNAc appeared to be significantly reduced in the quadruple rpf mutant. Collectively, our data have shown that Rpfs play an important role in biofilm formation, possibly through alterations in PG cross-linking and the production of signaling molecules.IMPORTANCE The cell wall of pathogenic mycobacteria is composed of peptidoglycan, arabinogalactan, mycolic acids, and an outer capsule. This inherent complexity renders it resistant to many antibiotics. Consequently, its biosynthesis and remodeling during growth directly impact viability. Resuscitation-promoting factors (Rpfs), enzymes with lytic transglycosylase activity, have been associated with the revival of dormant cells and subsequent resumption of vegetative growth. Mycobacterium smegmatis, a soil saprophyte and close relative of the human pathogen Mycobacterium tuberculosis, encodes four distinct Rpfs. Herein, we assessed the relationship between Rpfs and biofilm formation, which is used as a model to study drug tolerance and bacterial signaling in mycobacteria. We demonstrated that progressive deletion of rpf genes hampered the development of biofilms and reduced drug tolerance. These effects were accompanied by a reduction in muropeptide production and altered peptidoglycan cross-linking. Collectively, these observations point to an important role for Rpfs in mycobacterial communication and drug tolerance.
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146
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Kell DB, Pretorius E. No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases. Biol Rev Camb Philos Soc 2018; 93:1518-1557. [PMID: 29575574 PMCID: PMC6055827 DOI: 10.1111/brv.12407] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/12/2018] [Accepted: 02/15/2018] [Indexed: 12/11/2022]
Abstract
Since the successful conquest of many acute, communicable (infectious) diseases through the use of vaccines and antibiotics, the currently most prevalent diseases are chronic and progressive in nature, and are all accompanied by inflammation. These diseases include neurodegenerative (e.g. Alzheimer's, Parkinson's), vascular (e.g. atherosclerosis, pre-eclampsia, type 2 diabetes) and autoimmune (e.g. rheumatoid arthritis and multiple sclerosis) diseases that may appear to have little in common. In fact they all share significant features, in particular chronic inflammation and its attendant inflammatory cytokines. Such effects do not happen without underlying and initially 'external' causes, and it is of interest to seek these causes. Taking a systems approach, we argue that these causes include (i) stress-induced iron dysregulation, and (ii) its ability to awaken dormant, non-replicating microbes with which the host has become infected. Other external causes may be dietary. Such microbes are capable of shedding small, but functionally significant amounts of highly inflammagenic molecules such as lipopolysaccharide and lipoteichoic acid. Sequelae include significant coagulopathies, not least the recently discovered amyloidogenic clotting of blood, leading to cell death and the release of further inflammagens. The extensive evidence discussed here implies, as was found with ulcers, that almost all chronic, infectious diseases do in fact harbour a microbial component. What differs is simply the microbes and the anatomical location from and at which they exert damage. This analysis offers novel avenues for diagnosis and treatment.
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Affiliation(s)
- Douglas B. Kell
- School of ChemistryThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- The Manchester Institute of BiotechnologyThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
| | - Etheresia Pretorius
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
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147
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Antonova AV, Gryadunov DA, Zimenkov DV. Molecular Mechanisms of Drug Tolerance in Mycobacterium tuberculosis. Mol Biol 2018. [DOI: 10.1134/s0026893318030020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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148
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Chen YE, Fischbach MA, Belkaid Y. Skin microbiota-host interactions. Nature 2018; 553:427-436. [PMID: 29364286 DOI: 10.1038/nature25177] [Citation(s) in RCA: 375] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/28/2017] [Indexed: 12/23/2022]
Abstract
The skin is a complex and dynamic ecosystem that is inhabited by bacteria, archaea, fungi and viruses. These microbes-collectively referred to as the skin microbiota-are fundamental to skin physiology and immunity. Interactions between skin microbes and the host can fall anywhere along the continuum between mutualism and pathogenicity. In this Review, we highlight how host-microbe interactions depend heavily on context, including the state of immune activation, host genetic predisposition, barrier status, microbe localization, and microbe-microbe interactions. We focus on how context shapes the complex dialogue between skin microbes and the host, and the consequences of this dialogue for health and disease.
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Affiliation(s)
- Y Erin Chen
- Department of Dermatology, University of California San Francisco, San Francisco, California, USA.,Department of Bioengineering and ChEM-H, Stanford University, Stanford, California, USA
| | - Michael A Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, California, USA
| | - Yasmine Belkaid
- NIAID Microbiome Program, National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland, USA.,Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland, USA
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149
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Spät P, Klotz A, Rexroth S, Maček B, Forchhammer K. Chlorosis as a Developmental Program in Cyanobacteria: The Proteomic Fundament for Survival and Awakening. Mol Cell Proteomics 2018; 17:1650-1669. [PMID: 29848780 DOI: 10.1074/mcp.ra118.000699] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/25/2018] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteria that do not fix atmospheric nitrogen gas survive prolonged periods of nitrogen starvation in a chlorotic, dormant state where cell growth and metabolism are arrested. Upon nutrient availability, these dormant cells return to vegetative growth within 2-3 days. This resuscitation process is highly orchestrated and relies on the stepwise reinstallation and activation of essential cellular structures and functions. We have been investigating the transition to chlorosis and the return to vegetative growth as a simple model of a cellular developmental process and a fundamental survival strategy in biology. In the present study, we used quantitative proteomics and phosphoproteomics to describe the proteomic landscape of a dormant cyanobacterium and its dynamics during the transition to vegetative growth. We identified intriguing alterations in the set of ribosomal proteins, in RuBisCO components, in the abundance of central regulators and predicted metabolic enzymes. We found O-phosphorylation as an abundant protein modification in the chlorotic state, specifically of metabolic enzymes and proteins involved in photosynthesis. Nondegraded phycobiliproteins were hyperphosphorylated in the chlorotic state. We provide evidence that hyperphosphorylation of the terminal rod linker CpcD increases the lifespan of phycobiliproteins during chlorosis.
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Affiliation(s)
- Philipp Spät
- From the ‡Interfaculty Institute for Microbiology and Infection Medicine, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,¶Proteome Center Tuebingen, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Alexander Klotz
- From the ‡Interfaculty Institute for Microbiology and Infection Medicine, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Sascha Rexroth
- §Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Boris Maček
- ¶Proteome Center Tuebingen, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Karl Forchhammer
- From the ‡Interfaculty Institute for Microbiology and Infection Medicine, Eberhard-Karls University Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
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150
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Chai Q, Zhang Y, Liu CH. Mycobacterium tuberculosis: An Adaptable Pathogen Associated With Multiple Human Diseases. Front Cell Infect Microbiol 2018; 8:158. [PMID: 29868514 PMCID: PMC5962710 DOI: 10.3389/fcimb.2018.00158] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/25/2018] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis, the etiological agent of tuberculosis (TB), is an extremely successful pathogen that adapts to survive within the host. During the latency phase of infection, M. tuberculosis employs a range of effector proteins to be cloud the host immune system and shapes its lifestyle to reside in granulomas, sophisticated, and organized structures of immune cells that are established by the host in response to persistent infection. While normally being restrained in immunocompetent hosts, M. tuberculosis within granulomas can cause the recrudescence of TB when host immunity is compromised. Aside from causing TB, accumulating evidence suggests that M. tuberculosis is also associated with multiple other human diseases, such as pulmonary complications, autoimmune diseases, and metabolic syndromes. Furthermore, it has been recently appreciated that M. tuberculosis infection can also reciprocally interact with the human microbiome, which has a strong link to immune balance and health. In this review, we highlight the adaptive survival of M. tuberculosis within the host and provide an overview for regulatory mechanisms underlying interactions between M. tuberculosis infection and multiple important human diseases. A better understanding of how M. tuberculosis regulates the host immune system to cause TB and reciprocally regulates other human diseases is critical for developing rational treatments to better control TB and help alleviate its associated comorbidities.
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Affiliation(s)
- Qiyao Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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