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Comba-González NB, Chaves-Moreno D, Santamaría-Vanegas J, Montoya-Castaño D. A pan-genomic assessment: Delving into the genome of the marine epiphyte Bacillus altitudinis strain 19_A and other very close Bacillus strains from multiple environments. Heliyon 2024; 10:e27820. [PMID: 38560215 PMCID: PMC10981035 DOI: 10.1016/j.heliyon.2024.e27820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.
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Affiliation(s)
| | - Diego Chaves-Moreno
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Dolly Montoya-Castaño
- Bioprocesses and Bioprospecting Group, Biotechnology Institute, Universidad Nacional de Colombia, Colombia
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2
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Chen D, Yin Y, Hu Y, Cao L, Zhao C, Li B. Transposon-aided capture (TRACA) of plasmids from the human gut. Lett Appl Microbiol 2023; 76:ovad132. [PMID: 38031336 DOI: 10.1093/lambio/ovad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023]
Abstract
The gut microbiota consists of a vast and diverse assemblage of microorganisms that play a pivotal role in maintaining host health. Nevertheless, a significant portion of the human gut microbiota remains uncultivated. Plasmids, a type of MGE, assume a critical function in the biological evolution and adaptation of bacteria to varying environments. To investigate the plasmids present within the gut microbiota community, we used the transposon-aided capture method (TRACA) to explore plasmids derived from the gut microbiota. In this study, fecal samples were collected from two healthy human volunteers and subsequently subjected to the TRACA method for plasmid isolation. Then, the complete sequence of the plasmids was obtained using the genome walking method, and sequence identity was also analyzed. A total of 15 plasmids were isolated. At last, 13 plasmids were successfully sequenced, of which 12 plasmids were highly identical to the plasmids in the National Center for Biotechnology Information (NCBI) database and were all small plasmids. Furthermore, a putative novel plasmid, named pMRPHD, was isolated, which had mobilized elements (oriT and oriV) and a potential type II restriction-modification (R-M) system encoded by DNA cytosine methyltransferase and type II restriction enzyme (Ban I), whose specific functions and applications warrant further exploration.
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Affiliation(s)
- Dan Chen
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Yeshi Yin
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Yunfei Hu
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Linyan Cao
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Changhui Zhao
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Baiyuan Li
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
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3
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Kwun MS, Lee DG. Ferroptosis-Like Death in Microorganisms: A Novel Programmed Cell Death Following Lipid Peroxidation. J Microbiol Biotechnol 2023; 33:992-997. [PMID: 37463851 PMCID: PMC10471485 DOI: 10.4014/jmb.2307.07002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/20/2023]
Abstract
Ferroptosis is a new kind of programmed cell death of which occurrence in microorganisms is not clearly verified. The elevated level of reactive oxygen species (ROS) influences cellular metabolisms through highly reactive hydroxyl radical formation under the iron-dependent Fenton reaction. Iron contributes to ROS production and acts as a cofactor for lipoxygenase to catalyze poly unsaturated fatty acid (PUFA) oxidation, exerting oxidative damage in cells. While ferroptosis is known to take place only in mammalian cells, recent studies discovered the possible ferroptosis-like death in few specific microorganisms. Capacity of integrating PUFA into intracellular membrane phospholipid has been considered as a key factor in bacterial or fungal ferroptosis-like death. Vibrio species in bacteria and Saccharomyces cerevisiae in fungi exhibited certain characteristics. Therefore, this review focus on introducing the occurrence of ferroptosis-like death in microorganisms and investigating the mode of action underlying the cells based on contribution of lipid peroxidation and iron-dependent reaction.
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Affiliation(s)
- Min Seok Kwun
- School of Life Sciences, BK 21 FOUR KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daehakro 80, Bukgu, Daegu 41566, Republic of Korea
| | - Dong Gun Lee
- School of Life Sciences, BK 21 FOUR KNU Creative BioResearch Group, College of Natural Sciences, Kyungpook National University, Daehakro 80, Bukgu, Daegu 41566, Republic of Korea
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Kirillov A, Morozova N, Kozlova S, Polinovskaya V, Smirnov S, Khodorkovskii M, Zeng L, Ispolatov Y, Severinov K. Cells with stochastically increased methyltransferase to restriction endonuclease ratio provide an entry for bacteriophage into protected cell population. Nucleic Acids Res 2022; 50:12355-12368. [PMID: 36477901 PMCID: PMC9757035 DOI: 10.1093/nar/gkac1124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
The action of Type II restriction-modification (RM) systems depends on restriction endonuclease (REase), which cleaves foreign DNA at specific sites, and methyltransferase (MTase), which protects host genome from restriction by methylating the same sites. We here show that protection from phage infection increases as the copy number of plasmids carrying the Type II RM Esp1396I system is increased. However, since increased plasmid copy number leads to both increased absolute intracellular RM enzyme levels and to a decreased MTase/REase ratio, it is impossible to determine which factor determines resistance/susceptibility to infection. By controlled expression of individual Esp1396I MTase or REase genes in cells carrying the Esp1396I system, we show that a shift in the MTase to REase ratio caused by overproduction of MTase or REase leads, respectively, to decreased or increased protection from infection. Consistently, due to stochastic variation of MTase and REase amount in individual cells, bacterial cells that are productively infected by bacteriophage have significantly higher MTase to REase ratios than cells that ward off the infection. Our results suggest that cells with transiently increased MTase to REase ratio at the time of infection serve as entry points for unmodified phage DNA into protected bacterial populations.
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Affiliation(s)
- Alexander Kirillov
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia,Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Natalia Morozova
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia,Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Svetlana Kozlova
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia
| | - Vasilisa Polinovskaya
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia
| | - Sergey Smirnov
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow 121205, Russia
| | - Mikhail Khodorkovskii
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Lanying Zeng
- Texas A&M University, Department of Biochemistry and Biophysics, Center for Phage Technology, College Station, TX 77843, USA
| | - Yaroslav Ispolatov
- University of Santiago of Chile (USACH), Physics Department, Av. Víctor Jara 3493, Santiago, Chile
| | - Konstantin Severinov
- To whom correspondence should be addressed. Tel: +7 9854570284; Fax: +1 848 445 5735;
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Dorawa S, Werbowy O, Plotka M, Kaczorowska AK, Makowska J, Kozlowski LP, Fridjonsson OH, Hreggvidsson GO, Aevarsson A, Kaczorowski T. Molecular Characterization of a DNA Polymerase from Thermus thermophilus MAT72 Phage vB_Tt72: A Novel Type-A Family Enzyme with Strong Proofreading Activity. Int J Mol Sci 2022; 23:ijms23147945. [PMID: 35887293 PMCID: PMC9324360 DOI: 10.3390/ijms23147945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022] Open
Abstract
We present a structural and functional analysis of the DNA polymerase of thermophilic Thermus thermophilus MAT72 phage vB_Tt72. The enzyme shows low sequence identity (<30%) to the members of the type-A family of DNA polymerases, except for two yet uncharacterized DNA polymerases of T. thermophilus phages: φYS40 (91%) and φTMA (90%). The Tt72 polA gene does not complement the Escherichia colipolA− mutant in replicating polA-dependent plasmid replicons. It encodes a 703-aa protein with a predicted molecular weight of 80,490 and an isoelectric point of 5.49. The enzyme contains a nucleotidyltransferase domain and a 3′-5′ exonuclease domain that is engaged in proofreading. Recombinant enzyme with His-tag at the N-terminus was overproduced in E. coli, subsequently purified by immobilized metal affinity chromatography, and biochemically characterized. The enzyme exists in solution in monomeric form and shows optimum activity at pH 8.5, 25 mM KCl, and 0.5 mM Mg2+. Site-directed analysis proved that highly-conserved residues D15, E17, D78, D180, and D184 in 3′-5′ exonuclease and D384 and D615 in the nucleotidyltransferase domain are critical for the enzyme’s activity. Despite the source of origin, the Tt72 DNA polymerase has not proven to be highly thermoresistant, with a temperature optimum at 55 °C. Above 60 °C, the rapid loss of function follows with no activity > 75 °C. However, during heat treatment (10 min at 75 °C), trehalose, trimethylamine N-oxide, and betaine protected the enzyme against thermal inactivation. A midpoint of thermal denaturation at Tm = 74.6 °C (ΔHcal = 2.05 × 104 cal mol−1) and circular dichroism spectra > 60 °C indicate the enzyme’s moderate thermal stability.
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Affiliation(s)
- Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland; (S.D.); (O.W.); (M.P.)
| | - Olesia Werbowy
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland; (S.D.); (O.W.); (M.P.)
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland; (S.D.); (O.W.); (M.P.)
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland;
| | - Joanna Makowska
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
| | - Lukasz P. Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland;
| | | | - Gudmundur O. Hreggvidsson
- Matis, 113 Reykjavik, Iceland; (O.H.F.); (G.O.H.); (A.A.)
- Department of Biology, School of Engineering and Natural Sciences, University of Iceland, 102 Reykjavik, Iceland
| | | | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland; (S.D.); (O.W.); (M.P.)
- Correspondence:
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Zhang N, He J, Muhammad A, Shao Y. CRISPR/Cas9–Mediated Genome Editing for Pseudomonas fulva, a Novel Pseudomonas Species with Clinical, Animal, and Plant–Associated Isolates. Int J Mol Sci 2022; 23:ijms23105443. [PMID: 35628253 PMCID: PMC9145825 DOI: 10.3390/ijms23105443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 12/23/2022] Open
Abstract
As one of the most widespread groups of Gram–negative bacteria, Pseudomonas bacteria are prevalent in almost all natural environments, where they have developed intimate associations with plants and animals. Pseudomonas fulva is a novel species of Pseudomonas with clinical, animal, and plant–associated isolates, closely related to human and animal health, plant growth, and bioremediation. Although genetic manipulations have been proven as powerful tools for understanding bacterial biological and biochemical characteristics and the evolutionary origins, native isolates are often difficult to genetically manipulate, thereby making it a time–consuming and laborious endeavor. Here, by using the CRISPR–Cas system, a versatile gene–editing tool with a two–plasmid strategy was developed for a native P. fulva strain isolated from the model organism silkworm (Bombyx mori) gut. We harmonized and detailed the experimental setup and clarified the optimal conditions for bacteria transformation, competent cell preparation, and higher editing efficiency. Furthermore, we provided some case studies, testing and validating this approach. An antibiotic–related gene, oqxB, was knocked out, resulting in the slow growth of the P. fulva deletion mutant in LB containing chloramphenicol. Fusion constructs with knocked–in gfp exhibited intense fluorescence. Altogether, the successful construction and application of new genetic editing approaches gave us more powerful tools to investigate the functionalities of the novel Pseudomonas species.
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Affiliation(s)
- Nan Zhang
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
| | - Jintao He
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
| | - Abrar Muhammad
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
| | - Yongqi Shao
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China (A.M.)
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, Hangzhou 310058, China
- Correspondence: ; Fax: +86-571-88982757
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Arai T, Aikawa S, Sudesh K, Kondo T, Kosugi A. Electrotransformation of thermophilic bacterium Caldimonas manganoxidans. J Microbiol Methods 2021; 192:106375. [PMID: 34793853 DOI: 10.1016/j.mimet.2021.106375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/12/2021] [Accepted: 11/12/2021] [Indexed: 12/22/2022]
Abstract
Caldimonas manganoxidans is a Gram-negative, thermophilic, bioplastic-producing bacterium that is a promising strain to overcome the drawbacks of existing bioplastic manufacturing methods. However, genetic manipulation of this species has not previously been studied. Here, we developed an optimized electrotransformation protocol for C. manganoxidans by screening conditions, including the bacterial growth phase, electroporation buffer, pulse strength, and recovery time. The optimized transformation protocol obtained (3.1 ± 0.78) × 108 colony-forming units/μg DNA of plasmid pBBR1MCS-2. High transformation efficiency was observed when using plasmid DNA isolated from C. manganoxidans. The DNA methylases of Escherichia coli did not affect the transformation efficiency of C. manganoxidans. The electrotransformation technique proposed here will be beneficial for the genetic manipulation of thermophilic Caldimonas species.
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Affiliation(s)
- Takamitsu Arai
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi Tsukuba, Ibaraki 305-8686, Japan
| | - Shimpei Aikawa
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi Tsukuba, Ibaraki 305-8686, Japan
| | - Kumar Sudesh
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Toshiaki Kondo
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi Tsukuba, Ibaraki 305-8686, Japan
| | - Akihiko Kosugi
- Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi Tsukuba, Ibaraki 305-8686, Japan.
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Wilkowska K, Mruk I, Furmanek-Blaszk B, Sektas M. Low-level expression of the Type II restriction-modification system confers potent bacteriophage resistance in Escherichia coli. DNA Res 2021; 27:5804985. [PMID: 32167561 PMCID: PMC7315355 DOI: 10.1093/dnares/dsaa003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/09/2020] [Indexed: 01/21/2023] Open
Abstract
Restriction–modification systems (R–M) are one of the antiviral defense tools used by bacteria, and those of the Type II family are composed of a restriction endonuclease (REase) and a DNA methyltransferase (MTase). Most entering DNA molecules are usually cleaved by the REase before they can be methylated by MTase, although the observed level of fragmented DNA may vary significantly. Using a model EcoRI R–M system, we report that the balance between DNA methylation and cleavage may be severely affected by transcriptional signals coming from outside the R–M operon. By modulating the activity of the promoter, we obtained a broad range of restriction phenotypes for the EcoRI R–M system that differed by up to 4 orders of magnitude in our biological assays. Surprisingly, we found that high expression levels of the R–M proteins were associated with reduced restriction of invading bacteriophage DNA. Our results suggested that the regulatory balance of cleavage and methylation was highly sensitive to fluctuations in transcriptional signals both up- and downstream of the R–M operon. Our data provided further insights into Type II R–M system maintenance and the potential conflict within the host bacterium.
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Affiliation(s)
- Karolina Wilkowska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Beata Furmanek-Blaszk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Marian Sektas
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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Randall SE, Martini MC, Zhou Y, Joubran SR, Shell SS. MamA essentiality in Mycobacterium smegmatis is explained by the presence of an apparent cognate restriction endonuclease. BMC Res Notes 2020; 13:462. [PMID: 32993774 PMCID: PMC7526240 DOI: 10.1186/s13104-020-05302-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/22/2020] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Restriction-Modification (R-M) systems are ubiquitous in bacteria and were considered for years as rudimentary immune systems that protect bacterial cells from foreign DNA. Currently, these R-M systems are recognized as important players in global gene expression and other cellular processes such us virulence and evolution of genomes. Here, we report the role of the unique DNA methyltransferase in Mycobacterium smegmatis, which shows a moderate degree of sequence similarity to MamA, a previously characterized methyltransferase that affects gene expression in Mycobacterium tuberculosis and is important for survival under hypoxic conditions. RESULTS We found that depletion of mamA levels impairs growth and produces elongated cell bodies. Microscopy revealed irregular septation and unevenly distributed DNA, with large areas devoid of DNA and small DNA-free cells. Deletion of MSMEG_3214, a predicted endonuclease-encoding gene co-transcribed with mamA, restored the WT growth phenotype in a mamA-depleted background. Our results suggest that the mamA-depletion phenotype can be explained by DNA cleavage by the apparent cognate restriction endonuclease MSMEG_3214. In addition, in silico analysis predicts that both MamA methyltransferase and MSMEG_3214 endonuclease recognize the same palindromic DNA sequence. We propose that MamA and MSMEG_3214 constitute a previously undescribed R-M system in M. smegmatis.
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Affiliation(s)
- Samantha E Randall
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Maria Carla Martini
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Ying Zhou
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Samantha R Joubran
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Scarlet S Shell
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA. .,Program in Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA, USA.
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Ruess J, Pleška M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Comput Biol 2019; 15:e1007168. [PMID: 31265463 PMCID: PMC6629147 DOI: 10.1371/journal.pcbi.1007168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 07/15/2019] [Accepted: 06/07/2019] [Indexed: 01/21/2023] Open
Abstract
Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems.
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Affiliation(s)
- Jakob Ruess
- Inria Saclay - Ile-de-France, 91120 Palaiseau, France
- Institut Pasteur, USR 3756 IP CNRS, 75015 Paris, France
| | - Maroš Pleška
- Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria
- Rockefeller University, New York, New York, United States of America
| | - Cǎlin C. Guet
- Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria
| | - Gašper Tkačik
- Institute of Science and Technology Austria, A-3400 Klosterneuburg, Austria
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