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Albert P, Varga B, Ferenc G, Kiss A. Conversion of the CG specific M.MpeI DNA methyltransferase into an enzyme predominantly methylating CCA and CCC sites. Nucleic Acids Res 2024; 52:1896-1908. [PMID: 38164970 PMCID: PMC10899764 DOI: 10.1093/nar/gkad1217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
We used structure guided mutagenesis and directed enzyme evolution to alter the specificity of the CG specific bacterial DNA (cytosine-5) methyltransferase M.MpeI. Methylation specificity of the M.MpeI variants was characterized by digestions with methylation sensitive restriction enzymes and by measuring incorporation of tritiated methyl groups into double-stranded oligonucleotides containing single CC, CG, CA or CT sites. Site specific mutagenesis steps designed to disrupt the specific contacts between the enzyme and the non-substrate base pair of the target sequence (5'-CG/5'-CG) yielded M.MpeI variants with varying levels of CG specific and increasing levels of CA and CC specific MTase activity. Subsequent random mutagenesis of the target recognizing domain coupled with selection for non-CG specific methylation yielded a variant, which predominantly methylates CC dinucleotides, has very low activity on CG and CA sites, and no activity on CT sites. This M.MpeI variant contains a one amino acid deletion (ΔA323) and three substitutions (N324G, R326G and E305N) in the target recognition domain. The mutant enzyme has very strong preference for A and C in the 3' flanking position making it a CCA and CCC specific DNA methyltransferase.
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Affiliation(s)
- Pál Albert
- Laboratory of DNA-Protein Interactions, Institute of Biochemistry, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Bence Varga
- Laboratory of DNA-Protein Interactions, Institute of Biochemistry, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
- Nucleic Acid Synthesis Laboratory, Institute of Plant Biology, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
| | - Györgyi Ferenc
- Nucleic Acid Synthesis Laboratory, Institute of Plant Biology, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
| | - Antal Kiss
- Laboratory of DNA-Protein Interactions, Institute of Biochemistry, HUN-REN Biological Research Centre, 6726 Szeged, Hungary
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2
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Wang J, Li Y, Jaramillo-Torres A, Einen O, Jakobsen JV, Krogdahl Å, Kortner TM. Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics. Anim Microbiome 2023; 5:47. [PMID: 37789427 PMCID: PMC10548677 DOI: 10.1186/s42523-023-00269-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/24/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND The importance of the gut microbiota for physiological processes in mammals is well established, but the knowledge of their functional roles in fish is still limited. The aims of this study were to investigate associations between variation in taxonomical composition of the gut microbiota and gut health status in Atlantic salmon and to explore possible modulatory effects of dietary prebiotics in one net-pen farm in open water. The fish with initial mean body weight of around 240 g were fed diets based on the same basal composition, either without (Ref diet) or with (Test diet) yeast cell wall based-prebiotics, during the marine production phase from December to September the following year. Sampling was conducted at three sampling time points: January, April, and September, with average water temperature of 3.9 ℃, 3.4 ℃ and 9.6 ℃, respectively. RESULTS As the fish progressed towards September, growth, brush border membrane enzyme activities, and the expression in the gut of most of the observed genes involved in immune (e.g., il8, cd4a, myd88, il1b, gilt, tgfb, cd8b and cd3), barrier (e.g., zo1, occludin, ecad, claudin25b and claudin15), and metabolism increased significantly. Lipid accumulation in pyloric enterocytes decreased remarkably, suggesting improvement of gut health condition. The growth of the fish did not differ between dietary treatments. Further, dietary prebiotics affected the gut health only marginally regardless of duration of administration. Regarding gut microbiota composition, a decrease in alpha diversity (Observed species, Pielou and Shannon) over time was observed, which was significantly associated with an increase in the relative abundance of genus Mycoplasma and decrease in 32 different taxa in genus level including lactic acid bacteria (LAB), such as Lactobacillus, Leuconostoc, and Lactococcus. This indicates that developmental stage of Atlantic salmon is a determinant for microbial composition. Multivariate association analysis revealed that the relative abundance of Mycoplasma was positively correlated with gut barrier gene expression, negatively correlated with plasma glucose levels, and that its relative abundance slightly increased by exposure to prebiotics. Furthermore, certain LAB (e.g., Leuconostoc), belonging to the core microbiota, showed a negative development with time, and significant associations with plasma nutrients levels (e.g., triglyceride and cholesterol) and gene expression related to gut immune and barrier function. CONCLUSIONS As Atlantic salmon grew older under large-scale, commercial farm settings, the Mycoplasma became more prominent with a concomitant decline in LAB. Mycoplasma abundance correlated positively with time and gut barrier genes, while LAB abundance negatively correlated to time. Dietary prebiotics affected gut health status only marginally.
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Affiliation(s)
- Jie Wang
- National Aquafeed Safety Assessment Center, Institute of Feed Research, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South St, Beijing, China.
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway.
| | - Yanxian Li
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway
| | | | - Olai Einen
- Cermaq Group AS, Dronning Eufemias gate 16, Oslo, 0191, Norway
| | - Jan Vidar Jakobsen
- Cargill Aqua Nutrition, Prof. Olav Hanssensvei 7A, Stavanger, 4021, Norway
| | - Åshild Krogdahl
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway
| | - Trond M Kortner
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, Ås, 1432, Norway
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3
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Nakane D. Rheotaxis in Mycoplasma gliding. Microbiol Immunol 2023; 67:389-395. [PMID: 37430383 DOI: 10.1111/1348-0421.13090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
This review describes the upstream-directed movement in the small parasitic bacterium Mycoplasma. Many Mycoplasma species exhibit gliding motility, a form of biological motion over surfaces without the aid of general surface appendages such as flagella. The gliding motility is characterized by a constant unidirectional movement without changes in direction or backward motion. Unlike flagellated bacteria, Mycoplasma lacks the general chemotactic signaling system to control their moving direction. Therefore, the physiological role of directionless travel in Mycoplasma gliding remains unclear. Recently, high-precision measurements under an optical microscope have revealed that three species of Mycoplasma exhibited rheotaxis, that is, the direction of gliding motility is lead upstream by the water flow. This intriguing response appears to be optimized for the flow patterns encountered at host surfaces. This review provides a comprehensive overview of the morphology, behavior, and habitat of Mycoplasma gliding, and discusses the possibility that the rheotaxis is ubiquitous among them.
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Affiliation(s)
- Daisuke Nakane
- Department of Engineering Science, Graduate School of Informatics and Engineering, Tokyo, Japan
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Schwab NR, Young NE, Nzenwata DU, Toh E, Mikulin JA, Wilson TJ, Nelson DE, Balish MF. Characterization of Virulence-Associated Traits in Mycoplasma penetrans Strains Acting as Likely Etiological Agents of Idiopathic Nongonococcal Urethritis. J Infect Dis 2023; 227:1050-1058. [PMID: 36588346 PMCID: PMC10319971 DOI: 10.1093/infdis/jiac505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
Mycoplasma penetrans is an emerging pathogen with a reduced genome. This bacterium has only previously been cultured from individuals with chronic immunodeficiencies. Here we report the characteristics of 4 M. penetrans isolates from the urine of immunocompetent males with nongonococcal urethritis, in comparison with strain HF-2 from an immunocompromised patient. Several features exhibited distinct differences between these isolates and HF-2. Unlike HF-2, all 4 were resistant to azithromycin. They exhibited greater sialic acid-dependent binding to erythrocytes, gliding motility speed, and H2O2 production than HF-2. All new isolates produced thinner capsules than HF-2. Invasiveness varied, with some isolates being more invasive than HF-2 and some less invasive. Cytotoxicity to HeLa cells was similar to HF-2, and all strains could clear extracellular traps produced by innate immune cells. We conclude that subtle differences among M. penetrans strains may be critical for this organism to establish an infection in an otherwise healthy individual.
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Affiliation(s)
- Nathan R Schwab
- Department of Microbiology, Miami University, Oxford, Ohio, USA
| | - Natalie E Young
- Department of Microbiology, Miami University, Oxford, Ohio, USA
| | | | - Evelyn Toh
- Department of Microbiology and Immunology, School of Medicine, Indiana University, Indianapolis, Indiana, USA
| | | | | | - David E Nelson
- Department of Microbiology and Immunology, School of Medicine, Indiana University, Indianapolis, Indiana, USA
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Liu P, Li Y, Ye Y, Chen J, Li R, Zhang Q, Li Y, Wang W, Meng Q, Ou J, Yang Z, Sun W, Gu W. The genome and antigen proteome analysis of Spiroplasma mirum. Front Microbiol 2022; 13:996938. [PMID: 36406404 PMCID: PMC9666726 DOI: 10.3389/fmicb.2022.996938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023] Open
Abstract
Spiroplasma mirum, small motile wall-less bacteria, was originally isolated from a rabbit tick and had the ability to infect newborn mice and caused cataracts. In this study, the whole genome and antigen proteins of S. mirum were comparative analyzed and investigated. Glycolysis, pentose phosphate pathway, arginine metabolism, nucleotide biosynthesis, and citrate fermentation were found in S. mirum, while trichloroacetic acid, fatty acids metabolism, phospholipid biosynthesis, terpenoid biosynthesis, lactose-specific PTS, and cofactors synthesis were completely absent. The Sec systems of S. mirum consist of SecA, SecE, SecDF, SecG, SecY, and YidC. Signal peptidase II was identified in S. mirum, but no signal peptidase I. The relative gene order in S. mirum is largely conserved. Genome analysis of available species in Mollicutes revealed that they shared only 84 proteins. S. mirum genome has 381 pseudogenes, accounting for 31.6% of total protein-coding genes. This is the evidence that spiroplasma genome is under an ongoing genome reduction. Immunoproteomics, a new scientific technique combining proteomics and immunological analytical methods, provided the direction of our research on S. mirum. We identified 49 proteins and 11 proteins (9 proteins in common) in S. mirum by anti-S. mirum serum and negative serum, respectively. Forty proteins in S. mirum were identified in relation to the virulence. All these proteins may play key roles in the pathogeny and can be used in the future for diagnoses and prevention.
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Affiliation(s)
- Peng Liu
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Yuxin Li
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Youyuan Ye
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Jiaxin Chen
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Rong Li
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Qinyi Zhang
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Yuan Li
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Wen Wang
- Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
| | - Qingguo Meng
- Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
| | - Jingyu Ou
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Zhujun Yang
- Hunan Provincial Key Laboratory for Special Pathogens Prevention and Control, Basic Medical School, Hengyang Medical School, Institute of Pathogenic Biology, University of South China, Hengyang, China
| | - Wei Sun
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Wei Gu
- Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, China
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Complete Genomic Sequence of the Thermophilic Hydrogen-Oxidizing Methanogen Methanothermobacter tenebrarum Strain RMAS
T. Microbiol Resour Announc 2022; 11:e0035522. [PMID: 35861551 PMCID: PMC9302168 DOI: 10.1128/mra.00355-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanothermobacter tenebrarum strain RMAST has a complete genomic length of 1,472,762 bp, a GC content of 42.1%, 1,599 coding DNA sequences (CDSs), 1 CRISPR array, 3 rRNAs, and 38 tRNAs.
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Nakane D, Kabata Y, Nishizaka T. Cell shape controls rheotaxis in small parasitic bacteria. PLoS Pathog 2022; 18:e1010648. [PMID: 35834494 PMCID: PMC9282661 DOI: 10.1371/journal.ppat.1010648] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022] Open
Abstract
Mycoplasmas, a group of small parasitic bacteria, adhere to and move across host cell surfaces. The role of motility across host cell surfaces in pathogenesis remains unclear. Here, we used optical microscopy to visualize rheotactic behavior in three phylogenetically distant species of Mycoplasma using a microfluidic chamber that enabled the application of precisely controlled fluid flow. We show that directional movements against fluid flow occur synchronously with the polarized cell orienting itself to be parallel against the direction of flow. Analysis of depolarized cells revealed that morphology itself functions as a sensor to recognize rheological properties that mimic those found on host-cell surfaces. These results demonstrate the vital role of cell morphology and motility in responding to mechanical forces encountered in the native environment. The small, parasitic bacterium Mycoplasma pneumoniae attaches to, and moves over, host cell surfaces. Adherence to host surfaces and motility are critical for the pathogenicity of M. pneumoniae. The role of motility by M. pneumoniae in vivo, however, is poorly understood. Host airways generate constant fluid flow toward the mouth as part of their defense against pathogens and irritants. Consequently, pulmonary invaders must counter the rheological forces found in host airways in order to successfully colonize the host. Here, we demonstrate that M. pneumoniae exhibits directional movement against fluid flow. These findings suggest there is a vital role for rheotactic motility that has evolved in order to overcome host defense mechanisms such as mucociliary clearance.
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Affiliation(s)
- Daisuke Nakane
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Tokyo, Japan
- * E-mail: (DN); (TN)
| | - Yoshiki Kabata
- Department of Physics, Gakushuin University, Tokyo, Japan
| | - Takayuki Nishizaka
- Department of Physics, Gakushuin University, Tokyo, Japan
- * E-mail: (DN); (TN)
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Fisunov GY, Pobeguts OV, Ladygina VG, Zubov AI, Galyamina MA, Kovalchuk SI, Ziganshin RK, Evsyutina DV, Matyushkina DS, Butenko IO, Bukato ON, Veselovsky VA, Semashko TA, Klimina KM, Levina GA, Barhatova OI, Rakovskaya IV. Thymidine utilisation pathway is a novel phenotypic switch of Mycoplasma hominis. J Med Microbiol 2022; 71. [PMID: 35037614 PMCID: PMC8895549 DOI: 10.1099/jmm.0.001468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Introduction. Mycoplasma hominis is a bacterium belonging to the class Mollicutes. It causes acute and chronic infections of the urogenital tract. The main features of this bacterium are an absence of cell wall and a reduced genome size (517-622 protein-encoding genes). Previously, we have isolated morphologically unknown M. hominis colonies called micro-colonies (MCs) from the serum of patients with inflammatory urogenital tract infection.Hypothesis. MCs are functionally different from the typical colonies (TCs) in terms of metabolism and cell division.Aim. To determine the physiological differences between MCs and TCs of M. hominis and elucidate the pathways of formation and growth of MCs by a comparative proteomic analysis of these two morphological forms.Methodology. LC-MS proteomic analysis of TCs and MCs using an Ultimate 3000 RSLC nanoHPLC system connected to a QExactive Plus mass spectrometer.Results. The study of the proteomic profiles of M. hominis colonies allowed us to reconstruct their energy metabolism pathways. In addition to the already known pentose phosphate and arginine deamination pathways, M. hominis can utilise ribose phosphate and deoxyribose phosphate formed by nucleoside catabolism as energy sources. Comparative proteomic HPLC-MS analysis revealed that the proteomic profiles of TCs and MCs were different. We assume that MC cells preferably utilised deoxyribonucleosides, particularly thymidine, as an energy source rather than arginine or ribonucleosides. Utilisation of deoxyribonucleosides is less efficient as compared with that of ribonucleosides and arginine in terms of energy production. Thymidine phosphorylase DeoA is one of the key enzymes of deoxyribonucleosides utilisation. We obtained a DeoA overexpressing mutant that exhibited a phenotype similar to that of MCs, which confirmed our hypothesis.Conclusion. In addition to the two known pathways for energy production (arginine deamination and the pentose phosphate pathway) M. hominis can use deoxyribonucleosides and ribonucleosides. MC cells demonstrate a reorganisation of energy metabolism: unlike TC cells, they preferably utilise deoxyribonucleosides, particularly thymidine, as an energy source rather than arginine or ribonucleosides. Thus MC cells enter a state of energy starvation, which helps them to survive under stress, and in particular, to be resistant to antibiotics.
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Affiliation(s)
- Gleb Yu Fisunov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Olga V Pobeguts
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Valentina G Ladygina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Alexandr I Zubov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Mariya A Galyamina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Sergey I Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Rustam K Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Daria V Evsyutina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Daria S Matyushkina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Ivan O Butenko
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Olga N Bukato
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Vladimir A Veselovsky
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Tatiana A Semashko
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Ksenia M Klimina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia.,Department of Biotechnology, Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Galina A Levina
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russia
| | - Olga I Barhatova
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russia
| | - Irina V Rakovskaya
- Gamaleya National Research Center of Epidemiology and Microbiology, Moscow, Russia
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Metal utilization in genome-reduced bacteria: Do human mycoplasmas rely on iron? Comput Struct Biotechnol J 2021; 19:5752-5761. [PMID: 34765092 PMCID: PMC8566771 DOI: 10.1016/j.csbj.2021.10.022] [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: 06/30/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/04/2022] Open
Abstract
Mycoplasmas are parasitic bacteria with streamlined genomes and complex nutritional requirements. Although iron is vital for almost all organisms, its utilization by mycoplasmas is controversial. Despite its minimalist nature, mycoplasmas can survive and persist within the host, where iron availability is rigorously restricted through nutritional immunity. In this review, we describe the putative iron-enzymes, transporters, and metalloregulators of four relevant human mycoplasmas. This work brings in light critical differences in the mycoplasma-iron interplay. Mycoplasma penetrans, the species with the largest genome (1.36 Mb), shows a more classic repertoire of iron-related proteins, including different enzymes using iron-sulfur clusters as well as iron storage and transport systems. In contrast, the iron requirement is less apparent in the three species with markedly reduced genomes, Mycoplasma genitalium (0.58 Mb), Mycoplasma hominis (0.67 Mb) and Mycoplasma pneumoniae (0.82 Mb), as they exhibit only a few proteins possibly involved in iron homeostasis. The multiple facets of iron metabolism in mycoplasmas illustrate the remarkable evolutive potential of these minimal organisms when facing nutritional immunity and question the dependence of several human-infecting species for iron. Collectively, our data contribute to better understand the unique biology and infective strategies of these successful pathogens.
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Key Words
- ABC, ATP-binding cassette
- ECF transporter
- ECF, energy-coupling factor
- Fur, ferric uptake regulator
- Hrl, histidine-rich lipoprotein
- Iron homeostasis
- Metal acquisition
- Metalloenzyme
- Mge, Mycoplasma genitalium
- Mho, Mycoplasma hominis
- Mollicutes
- Mpe, Mycoplasma penetrans
- Mpn, Mycoplasma pneumonia
- Mycoplasmas
- PDB, protein data bank
- RNR, ribonucleotide reductase
- XRF, X-ray fluorescence
- ZIP, zinc-iron permease
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Cheaib B, Yang P, Kazlauskaite R, Lindsay E, Heys C, Dwyer T, De Noa M, Schaal P, Sloan W, Ijaz U, Llewellyn M. Genome erosion and evidence for an intracellular niche - exploring the biology of mycoplasmas in Atlantic salmon. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2021; 541:736772. [PMID: 34471330 PMCID: PMC8192413 DOI: 10.1016/j.aquaculture.2021.736772] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/15/2021] [Accepted: 04/12/2021] [Indexed: 05/09/2023]
Abstract
Mycoplasmas are the smallest autonomously self-replicating life form on the planet. Members of this bacterial genus are known to parasitise a wide array of metazoans including vertebrates. Whilst much research has been significant targeted at parasitic mammalian mycoplasmas, very little is known about their role in other vertebrates. In the current study, we aim to explore the biology of mycoplasmas in Atlantic Salmon, a species of major significance for aquaculture, including cellular niche, genome size structure and gene content. Using fluorescent in-situ hybridisation (FISH), mycoplasmas were targeted in epithelial tissues across the digestive tract (stomach, pyloric caecum and midgut) from different development stages (eggs, parr, subadult) of farmed Atlantic salmon (Salmo salar), and we present evidence for an intracellular niche for some of the microbes visualised. Via shotgun metagenomic sequencing, a nearly complete, albeit small, genome (~0.57 MB) as assembled from a farmed Atlantic salmon subadult. Phylogenetic analysis of the recovered genome revealed taxonomic proximity to other salmon derived mycoplasmas, as well as to the human pathogen Mycoplasma penetrans (~1.36 Mb). We annotated coding sequences and identified riboflavin pathway encoding genes and sugar transporters, the former potentially consistent with micronutrient provisioning in salmonid development. Our study provides insights into mucosal adherence, the cellular niche and gene catalog of Mycoplasma in the gut ecosystem of the Atlantic salmon, suggesting a high dependency of this minimalist bacterium on its host. Further study is required to explore and functional role of Mycoplasma in the nutrition and development of its salmonid host.
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Affiliation(s)
- B. Cheaib
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
- School of Engineering, University of Glasgow, Glasgow G12 8QQ, United Kingdom
- Corresponding author at: Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
| | - P. Yang
- Laboratory of Aquaculture, nutrition and feed, Fisheries College, Ocean University of China, Hongdao Rd, Shinan District, Qingdao, Shandong, China
| | - R. Kazlauskaite
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - E. Lindsay
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - C. Heys
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - T. Dwyer
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - M. De Noa
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Patrick Schaal
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - W. Sloan
- School of Engineering, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - U.Z. Ijaz
- School of Engineering, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - M.S. Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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A Novel Aminoacyl-tRNA Synthetase Appended Domain Can Supply the Core Synthetase with Its Amino Acid Substrate. Genes (Basel) 2020; 11:genes11111320. [PMID: 33171705 PMCID: PMC7694997 DOI: 10.3390/genes11111320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 11/17/2022] Open
Abstract
The structural organization and functionality of aminoacyl-tRNA synthetases have been expanded through polypeptide additions to their core aminoacylation domain. We have identified a novel domain appended to the methionyl-tRNA synthetase (MetRS) of the intracellular pathogen Mycoplasma penetrans. Sequence analysis of this N-terminal region suggests the appended domain is an aminotransferase, which we demonstrate here. The aminotransferase domain of MpMetRS is capable of generating methionine from its α-keto acid analog, 2-keto-4-methylthiobutyrate (KMTB). The methionine thus produced can be subsequently attached to cognate tRNAMet in the MpMetRS aminoacylation domain. Genomic erosion in the Mycoplasma species has impaired many canonical biosynthetic pathways, causing them to rely on their host for numerous metabolites. It is still unclear if this bifunctional MetRS is a key part of pathogen life cycle or is a neutral consequence of the reductive evolution experienced by Mycoplasma species.
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Braymer JJ, Freibert SA, Rakwalska-Bange M, Lill R. Mechanistic concepts of iron-sulfur protein biogenesis in Biology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118863. [PMID: 33007329 DOI: 10.1016/j.bbamcr.2020.118863] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/08/2023]
Abstract
Iron-sulfur (Fe/S) proteins are present in virtually all living organisms and are involved in numerous cellular processes such as respiration, photosynthesis, metabolic reactions, nitrogen fixation, radical biochemistry, protein synthesis, antiviral defense, and genome maintenance. Their versatile functions may go back to the proposed role of their Fe/S cofactors in the origin of life as efficient catalysts and electron carriers. More than two decades ago, it was discovered that the in vivo synthesis of cellular Fe/S clusters and their integration into polypeptide chains requires assistance by complex proteinaceous machineries, despite the fact that Fe/S proteins can be assembled chemically in vitro. In prokaryotes, three Fe/S protein biogenesis systems are known; ISC, SUF, and the more specialized NIF. The former two systems have been transferred by endosymbiosis from bacteria to mitochondria and plastids, respectively, of eukaryotes. In their cytosol, eukaryotes use the CIA machinery for the biogenesis of cytosolic and nuclear Fe/S proteins. Despite the structural diversity of the protein constituents of these four machineries, general mechanistic concepts underlie the complex process of Fe/S protein biogenesis. This review provides a comprehensive and comparative overview of the various known biogenesis systems in Biology, and summarizes their common or diverging molecular mechanisms, thereby illustrating both the conservation and diverse adaptions of these four machineries during evolution and under different lifestyles. Knowledge of these fundamental biochemical pathways is not only of basic scientific interest, but is important for the understanding of human 'Fe/S diseases' and can be used in biotechnology.
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Affiliation(s)
- Joseph J Braymer
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | - Sven A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | | | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany; SYNMIKRO Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany.
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Kordafshari S, Shil P, Marenda MS, Olaogun OM, Konsak-Ilievski B, Disint J, Noormohammadi AH. Preliminary comparative analysis of the genomes of selected field reisolates of the Mycoplasma synoviae vaccine strain MS-H reveals both stable and unstable mutations after passage in vivo. BMC Genomics 2020; 21:598. [PMID: 32859151 PMCID: PMC7456371 DOI: 10.1186/s12864-020-06995-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023] Open
Abstract
Background Genomic comparison of Mycoplasma synoviae vaccine strain MS-H and the MS-H parental strain 86,079/7NS established a preliminary profile of genes related to attenuation of MS-H. In this study we aimed to identify the stability of mutations found in MS-H after passage in experimental or field chickens, and to evaluate if any reverse mutation may be associated with changes in characteristics of MS-H in vitro or in vivo. Results Whole genome sequence analysis of 5 selected MS-H field reisolates revealed that out of 32 mutations reported previously in MS-H, 28 remained stable, while four found to be reversible to the wild-type. Each isolate possessed mutations in one to three of the genes obg, oppF1 and gap and/or a non-coding region. Examination of the 4 reversible mutations by protein modeling predicted that only two of them (in obg and oppF1 genes) could potentially restore the function of the respective protein to that of the wild-type. Conclusions These results suggest that the majority of the MS-H mutations are stable after passage in vaccinated chickens. Characterisation of stable mutations found in MS-H could be utilised to develop rapid diagnostic techniques for differentiation of vaccine from field strains or ts- MS-H reisolates.
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Affiliation(s)
- Somayeh Kordafshari
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia.
| | - Pollob Shil
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - Marc S Marenda
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - Olusola M Olaogun
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - Barbara Konsak-Ilievski
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - Jillian Disint
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
| | - Amir H Noormohammadi
- Asia Pacific Centre for Animal Health, Faculty of Veterinary & Agricultural Sciences, The University of Melbourne, Werribee, Victoria, 3030, Australia
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Schuh LK, Weyler C, Heinzle E. In‐depth characterization of genome‐scale network reconstructions for the in vitro synthesis in cell‐free systems. Biotechnol Bioeng 2020; 117:1137-1147. [DOI: 10.1002/bit.27249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/25/2019] [Accepted: 12/06/2019] [Indexed: 01/15/2023]
Affiliation(s)
- Lisa Katharina Schuh
- Biochemical Engineering Institute Saarland University Campus A1.5 Saarbrücken Germany
| | - Christian Weyler
- Biochemical Engineering Institute Saarland University Campus A1.5 Saarbrücken Germany
| | - Elmar Heinzle
- Biochemical Engineering Institute Saarland University Campus A1.5 Saarbrücken Germany
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Preiswerk B, Imkamp F, Vorburger D, Hömke RV, Keller PM, Wagner K. Mycoplasma penetrans bacteremia in an immunocompromised patient detected by metagenomic sequencing: a case report. BMC Infect Dis 2020; 20:7. [PMID: 31900105 PMCID: PMC6942334 DOI: 10.1186/s12879-019-4723-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/22/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycoplasma sp. are well recognized as etiological agents of respiratory and sexually transmitted disease. Mycoplasma penetrans, a species of Mycoplasma sp., has been frequently detected in HIV-positive patients and associated with the progression of HIV-associated disease. To date, there is only a single case report describing M. penetrans as the causative agent of a severe respiratory tract infection in a HIV-negative patient. CASE PRESENTATION In this report, we describe the case of M. penetrans bacteremia in a HIV-negative, 38-year-old, female, immunocompromised, solid organ transplant patient (combined kidney and pancreas transplantation in 2016), who was admitted to our hospital with anemic uterine bleeding and fever of 38.3 °C. Several hours before her admission at our university hospital, a latex bladder catheter was inserted into her uterus and she complained about fatigue, dizziness and ongoing vaginal bleeding. Laboratory examination showed severe anemia, but microbiological examination was inconspicuous (culture negative vaginal and cervical smears, negative urine culture). Bacterial blood cultures showed a growth signal after 4 h, but microscopic examination with Gram staining and subcultures on different agar media did not identify bacterial pathogens. To identify the bacterial cause of malignancy in the patient, metagenomic sequencing of the blood culture was performed that identified M. penetrans. CONCLUSION Metagenomic sequencing identified M. penetrans in an immunosuppressed patient with culture-negative bacteremia. Clinicians should be aware of the opportunistic potential of M. penetrans that may cause severe infections in certain vulnerable patient populations and the limitations of culture and Gram staining for confirming the presence of fastidious bacterial pathogens like Mycoplasma spp.
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Affiliation(s)
- Benjamin Preiswerk
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Present Address: Triemli Hospital Zurich, Zurich, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Denise Vorburger
- Department of Gynecology, University Hospital Zurich, Zurich, Switzerland
| | - Rico V. Hömke
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Peter M. Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Present Address: Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Karoline Wagner
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Laboratory Medicine, University Hospital of Basel, Petersgraben 4, 4031 Basel, Switzerland
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Talankova-Sereda TE, Kolomiets JV, Holubenko AV, Nuzhyna NV. The influence of clonal micropropagation on productivity and differentiation of Mentha pіperіta plant tissues. REGULATORY MECHANISMS IN BIOSYSTEMS 2019. [DOI: 10.15421/021952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Peppermint grass, as a raw medicinal plant material, has great importance for the pharmaceutical industry. The influence of clonal micropropagation and chemotherapy has been established in vitro on six breeds of Ukrainian selection peppermint plants, in particular on the sprouts’ conductive system structure and tissue development, general biomass accumulation, and in vivo productivity of breeds. The influence of clonal micropropagation and chemotherapy on important productivity indices of the plants has been established in vitro in six breeds of Ukrainian selection peppermint plants as pharmacopeial plants. The linear meter method, the microscopic method, the standard histochemical methods, and the statistical analysis method were used in the studies. A clear tendency to increase in the leaf cover, air-dry leafage and rhizome was observed in breeds of Ukrainian selection peppermint to which propagation and in vitro improvement technology was applied. The air-dry leafage yield significantly increased after in vitro culture from 7.6% in the Lidiia breed to 51.4% in the Chornolysta breed recognized as a state mint standard in Ukraine. The leaf cover increased from 8% to 21% in peppermint plants improved in іn vitro culture. This method promoted essential oil quantity increase from 9.8 to 28.6 kg per hectare. The rhizome yield increased by 6.3–40.4% in all peppermint plants breeds after improvement in in vitro culture on average within one vegetation year. The Lebedyna Pisnіa and Mama breeds were characterised by the most intensive development of all investigated anatomic and morphological indices after in vitro culture: rhizomes yield increased by 40.4% and 40.1%, air-dry leafage by 37.1% and 26.6%, leaf cover by 21.0% and 13.0%, and essential oil quantity per hectare increased by 38.1% and 28.5% accordingly. Anatomical and histochemical studies of sprouts of Ukrainian selection peppermint plants breeds confirmed increase in xylogenesis intensity in the majority of the studied breeds (except Lidiia and Ukrains’ka Pertseva) after in vitro culture improvement. The xylogenesis process was most expressed in the Mama and Chornolysta breeds. Air-dry leafage, rhizome yield, and leaf cover increased in all peppermint plants breeds after in vitro improvement, which could be critical for the pharmaceutical industry.
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Zhu L, Shahid MA, Markham J, Browning GF, Noormohammadi AH, Marenda MS. Comparative genomic analyses of Mycoplasma synoviae vaccine strain MS-H and its wild-type parent strain 86079/7NS: implications for the identification of virulence factors and applications in diagnosis of M. synoviae. Avian Pathol 2019; 48:537-548. [PMID: 31244324 DOI: 10.1080/03079457.2019.1637514] [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] [Indexed: 01/29/2023]
Abstract
Mycoplasma synoviae is an economically important avian pathogen worldwide, causing respiratory disease, infectious synovitis, airsacculitis and eggshell apex abnormalities in commercial chickens. Despite the widespread use of MS-H as a live attenuated vaccine over the past two decades, the precise molecular basis for loss of virulence in this vaccine is not yet fully understood. To address this, the whole genome sequence of the vaccine parent strain, 86079/7NS, was obtained and compared to that of the MS-H vaccine. Except for the vlhA expressed region, both genomes were nearly identical. Thirty-two single nucleotide polymorphisms (SNPs) were identified in MS-H, including 11 non-synonymous mutations that were predicted, by bioinformatics analysis, to have changed the secondary structure of the deduced proteins. One of these mutations caused truncation of the oppF-1 gene, which encodes the ATP-binding protein of an oligopeptide permease transporter. Overall, the attenuation of MS-H strain may be caused by the cumulative and complex effects of several mutations. The SNPs identified in MS-H were further analyzed by comparing the MS-H and 86079/7NS sequences with the strains WVU-1853 and MS53. In the genomic regions conserved between all strains, 30 SNPs were found to be unique to MS-H lineage. These results have provided a foundation for developing novel biomarkers for the detection of virulence in M. synoviae and also for designing new genotyping assays for discrimination of MS-H from field strains.
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Affiliation(s)
- Ling Zhu
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, the University of Melbourne , Werribee , Australia
| | - Muhammad A Shahid
- Department of Pathobiology, Faculty of Veterinary Sciences, Bahauddin Zakariya University , Multan , Pakistan
| | - John Markham
- Department of Electrical and Electronic Engineering, the University of Melbourne , Parkville , Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, the University of Melbourne , Parkville , Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, the University of Melbourne , Werribee , Australia
| | - Marc S Marenda
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, the University of Melbourne , Werribee , Australia
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Steury RA, Currey MC, Cresko WA, Bohannan BJM. Population Genetic Divergence and Environment Influence the Gut Microbiome in Oregon Threespine Stickleback. Genes (Basel) 2019; 10:E484. [PMID: 31248008 PMCID: PMC6678413 DOI: 10.3390/genes10070484] [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: 05/03/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 12/27/2022] Open
Abstract
Much of animal-associated microbiome research has been conducted in species for which little is known of their natural ecology and evolution. Microbiome studies that combine population genetic, environment, and geographic data for wild organisms can be very informative, especially in situations where host genetic variation and the environment both influence microbiome variation. The few studies that have related population genetic and microbiome variation in wild populations have been constrained by observation-based kinship data or incomplete genomic information. Here we integrate population genomic and microbiome analyses in wild threespine stickleback fish distributed throughout western Oregon, USA. We found that gut microbiome diversity and composition partitioned more among than within wild host populations and was better explained by host population genetic divergence than by environment and geography. We also identified gut microbial taxa that were most differentially abundant across environments and across genetically divergent populations. Our findings highlight the benefits of studies that investigate host-associated microbiomes in wild organisms.
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Affiliation(s)
- Robert A Steury
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
| | - Mark C Currey
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
| | - William A Cresko
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
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Roachford O, Nelson KE, Mohapatra BR. Virulence and molecular adaptation of human urogenital mycoplasmas: a review. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1607556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Orville Roachford
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | | | - Bidyut Ranjan Mohapatra
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
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20
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Li J, Li L, Jiang H, Yuan L, Zhang L, Ma JE, Zhang X, Cheng M, Chen J. Fecal Bacteriome and Mycobiome in Bats with Diverse Diets in South China. Curr Microbiol 2018; 75:1352-1361. [PMID: 29922970 DOI: 10.1007/s00284-018-1530-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 06/14/2018] [Indexed: 01/05/2023]
Abstract
Bats can be divided into frugivory, nectarivory, insectivory, and sanguivory based on their diets, and are therefore ideal wild animal models to study the relationship between diets and intestinal microflora. Early studies of bat gut bacteria showed that the diversity and structure of intestinal bacterial communities in bats are closely related to dietary changes. Worthy of note, intestinal microbes are composed of bacteria, fungi, protozoa, and archaea. Although the number of gut fungi is much lower than that of gut bacteria, they also play an important role in maintaining the host homeostasis. However, there are still few reports on the relationship between the gut mycobiota and the dietary habits of the host. In addition, bats have also been shown to naturally transmit pathogenic viruses and bacteria through their feces and saliva, but fungal infections from bat are less studied. Here, we used high-throughput sequencing of bacterial 16S and eukaryotic 18S rRNA genes in the V4 and V9 regions to characterize fecal bacterial and fungal microbiota in phytophagous and insectivorous bats in South China. The results show that the gut microbiota in bats were dominated by bacterial phyla Proteobacteria, Firmicutes, Tenericutes and Bacteroidetes, and fungal phyla Ascomycota and Basidiomycota. There was a significant difference in the diversity of bacterial and fungal microbiota between the groups, in addition to specific bacteria and fungi populations on each of them. Of note, the number of fungi in the feces of herbivorous bats is relatively higher. Most of these fungi are foodborne and are also pathogens of humans and other animals. Thus, bats are natural carriers of fungal pathogens. The current study expands the understanding of the bat gut bacterial and fungal mycobiota and provides further insight into the transmission of fungal pathogens.
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Affiliation(s)
- Juan Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, Guangdong, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, Guangzhou, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, Guangzhou, China
| | - Haiying Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Science, Guangzhou, 510650, Guangdong, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, Guangzhou, China
| | - Lihong Yuan
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, Guangzhou, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, Guangzhou, China
| | - Jing-E Ma
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, Guangzhou, China
| | - Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, Guangzhou, China
| | - Minhua Cheng
- Wuhan Chopper Biology Co., Ltd, Wuhan, 430000, Hubei, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, Guangzhou, China.
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Albert P, Varga B, Zsibrita N, Kiss A. Circularly permuted variants of two CG-specific prokaryotic DNA methyltransferases. PLoS One 2018; 13:e0197232. [PMID: 29746549 PMCID: PMC5944983 DOI: 10.1371/journal.pone.0197232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/27/2018] [Indexed: 01/06/2023] Open
Abstract
The highly similar prokaryotic DNA (cytosine-5) methyltransferases (C5-MTases) M.MpeI and M.SssI share the specificity of eukaryotic C5-MTases (5'-CG), and can be useful research tools in the study of eukaryotic DNA methylation and epigenetic regulation. In an effort to improve the stability and solubility of complementing fragments of the two MTases, genes encoding circularly permuted (CP) variants of M.MpeI and M.SssI were created, and cloned in a plasmid vector downstream of an arabinose-inducible promoter. MTase activity of the CP variants was tested by digestion of the plasmids with methylation-sensitive restriction enzymes. Eleven of the fourteen M.MpeI permutants and six of the seven M.SssI permutants had detectable MTase activity as indicated by the full or partial protection of the plasmid carrying the cpMTase gene. Permutants cp62M.MpeI and cp58M.SssI, in which the new N-termini are located between conserved motifs II and III, had by far the highest activity. The activity of cp62M.MpeI was comparable to the activity of wild-type M.MpeI. Based on the location of the split sites, the permutants possessing MTase activity can be classified in ten types. Although most permutation sites were designed to fall outside of conserved motifs, and the MTase activity of the permutants measured in cell extracts was in most cases substantially lower than that of the wild-type enzyme, the high proportion of circular permutation topologies compatible with MTase activity is remarkable, and is a new evidence for the structural plasticity of C5-MTases. A computer search of the REBASE database identified putative C5-MTases with CP arrangement. Interestingly, all natural circularly permuted C5-MTases appear to represent only one of the ten types of permutation topology created in this work.
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Affiliation(s)
- Pál Albert
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Bence Varga
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Nikolett Zsibrita
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Antal Kiss
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
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Comparative Metabolomics of Mycoplasma bovis and Mycoplasma gallisepticum Reveals Fundamental Differences in Active Metabolic Pathways and Suggests Novel Gene Annotations. mSystems 2017; 2:mSystems00055-17. [PMID: 29034329 PMCID: PMC5634790 DOI: 10.1128/msystems.00055-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/11/2017] [Indexed: 11/25/2022] Open
Abstract
Mycoplasmas are pathogenic bacteria that cause serious chronic infections in production animals, resulting in considerable losses worldwide, as well as causing disease in humans. These bacteria have extremely reduced genomes and are thought to have limited metabolic flexibility, even though they are highly successful persistent parasites in a diverse number of species. The extent to which different Mycoplasma species are capable of catabolizing host carbon sources and nutrients, or synthesizing essential metabolites, remains poorly defined. We have used advanced metabolomic techniques to identify metabolic pathways that are active in two species of Mycoplasma that infect distinct hosts (poultry and cattle). We show that these species exhibit marked differences in metabolite steady-state levels and carbon source utilization. This information has been used to functionally characterize previously unknown genes in the genomes of these pathogens. These species-specific differences are likely to reflect important differences in host nutrient levels and pathogenic mechanisms. Mycoplasmas are simple, but successful parasites that have the smallest genome of any free-living cell and are thought to have a highly streamlined cellular metabolism. Here, we have undertaken a detailed metabolomic analysis of two species, Mycoplasma bovis and Mycoplasma gallisepticum, which cause economically important diseases in cattle and poultry, respectively. Untargeted gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry analyses of mycoplasma metabolite extracts revealed significant differences in the steady-state levels of many metabolites in central carbon metabolism, while 13C stable isotope labeling studies revealed marked differences in carbon source utilization. These data were mapped onto in silico metabolic networks predicted from genome wide annotations. The analyses elucidated distinct differences, including a clear difference in glucose utilization, with a marked decrease in glucose uptake and glycolysis in M. bovis compared to M. gallisepticum, which may reflect differing host nutrient availabilities. The 13C-labeling patterns also revealed several functional metabolic pathways that were previously unannotated in these species, allowing us to assign putative enzyme functions to the products of a number of genes of unknown function, especially in M. bovis. This study demonstrates the considerable potential of metabolomic analyses to assist in characterizing significant differences in the metabolism of different bacterial species and in improving genome annotation. IMPORTANCE Mycoplasmas are pathogenic bacteria that cause serious chronic infections in production animals, resulting in considerable losses worldwide, as well as causing disease in humans. These bacteria have extremely reduced genomes and are thought to have limited metabolic flexibility, even though they are highly successful persistent parasites in a diverse number of species. The extent to which different Mycoplasma species are capable of catabolizing host carbon sources and nutrients, or synthesizing essential metabolites, remains poorly defined. We have used advanced metabolomic techniques to identify metabolic pathways that are active in two species of Mycoplasma that infect distinct hosts (poultry and cattle). We show that these species exhibit marked differences in metabolite steady-state levels and carbon source utilization. This information has been used to functionally characterize previously unknown genes in the genomes of these pathogens. These species-specific differences are likely to reflect important differences in host nutrient levels and pathogenic mechanisms.
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23
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Roachford OSE, Nelson KE, Mohapatra BR. Comparative genomics of four Mycoplasma species of the human urogenital tract: Analysis of their core genomes and virulence genes. Int J Med Microbiol 2017; 307:508-520. [PMID: 28927691 DOI: 10.1016/j.ijmm.2017.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/29/2017] [Accepted: 09/04/2017] [Indexed: 12/23/2022] Open
Abstract
The variation in Mycoplasma lipoproteins attributed to genome rearrangements and genetic insertions leads to phenotypic plasticity that allows for the evasion of the host's defence system and pathogenesis. This paper compared for the first time the genomes of four human urogenital Mycoplasma species (M. penetrans HF-2, M. fermentans JER, M. genitalium G37 and M. hominis PG21) to categorise the metabolic functions of the core genes and to assess the effects of tandem repeats, phage-like genetic elements and prophages on the virulence genes. The results of this comparative in silico genomic analysis revealed that the genes constituting their core genomes can be separated into three distinct categories: nuclear metabolism, protein metabolism and energy generation each making up 52%, 31% and 23%, respectively. The genomes have repeat sequences ranging from 3.7% in M. hominis PG21 to 9.5% in M. fermentans JER. Tandem repeats (mostly minisatellites) and phage-like proteins (including DNA gyrases/topoisomerases) were randomly distributed in the Mycoplasma genomes. Here, we identified a coiled-coil structure containing protein in M. penetrans HF-2 which is significantly similar to the Mem protein of M. fermentans ɸMFV1. Therefore, a Mycoplasma prophage seems to be embedded within M. penetrans HF-2 unannotated genome. To the best of our knowledge, no Mycoplasma phages or prophages have been detected in M. penetrans. This study is important not only in understanding the complex genetic factors involved in phenotypic plasticity and virulence in the relatively understudied Mycoplasma species but also in elucidating the effective arrangement of their redundant minimal genomes.
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Affiliation(s)
- Orville St E Roachford
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown BB 11000, Barbados.
| | - Karen E Nelson
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD 20850, USA
| | - Bidyut R Mohapatra
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown BB 11000, Barbados
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Naito M, Desirò A, González JB, Tao G, Morton JB, Bonfante P, Pawlowska TE. 'Candidatus Moeniiplasma glomeromycotorum', an endobacterium of arbuscular mycorrhizal fungi. Int J Syst Evol Microbiol 2017; 67:1177-1184. [PMID: 28073398 DOI: 10.1099/ijsem.0.001785] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF, subphylum Glomeromycotina) are symbionts of most terrestrial plants. They commonly harbour endobacteria of a largely unknown biology, referred to as MRE (Mollicutes/mycoplasma-related endobacteria). Here, we propose to accommodate MRE in the novel genus 'Candidatus Moeniiplasma.' Phylogeny reconstructions based on the 16S rRNA gene sequences cluster 'Ca.Moeniiplasma' with representatives of the class Mollicutes, whereas phylogenies derived from amino acid sequences of 19 genes indicate that it is a discrete lineage sharing ancestry with the members of the family Mycoplasmataceae. Cells of 'Ca.Moeniiplasma' reside directly in the host cytoplasm and have not yet been cultivated. They are coccoid, ~500 nm in diameter, with an electron-dense layer outside the plasma membrane. However, the draft genomes of 'Ca.Moeniiplasma' suggest that this structure is not a Gram-positive cell wall. The evolution of 'Ca.Moeniiplasma' appears to be driven by an ultrarapid rate of mutation accumulation related to the loss of DNA repair mechanisms. Moreover, molecular evolution patterns suggest that, in addition to vertical transmission, 'Ca.Moeniiplasma' is able to transmit horizontally among distinct Glomeromycotina host lineages and exchange genes. On the basis of these unique lifestyle features, the new species 'Candidatus Moeniiplasma glomeromycotorum' is proposed.
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Affiliation(s)
- Mizue Naito
- Graduate Field of Microbiology, Cornell University, Ithaca, NY, USA
| | - Alessandro Desirò
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.,Present address: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Jonathan B González
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
| | - Gang Tao
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, NY, USA.,Present address: Guizhou Academy of Agricultural Sciences, Guizhou Institute of Plant Protection, Guiyang 550006, PR China
| | - Joseph B Morton
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Teresa E Pawlowska
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
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The Variable Internal Structure of the Mycoplasma penetrans Attachment Organelle Revealed by Biochemical and Microscopic Analyses: Implications for Attachment Organelle Mechanism and Evolution. J Bacteriol 2017; 199:JB.00069-17. [PMID: 28373274 DOI: 10.1128/jb.00069-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/27/2017] [Indexed: 01/13/2023] Open
Abstract
Although mycoplasmas have small genomes, many of them, including the HIV-associated opportunist Mycoplasma penetrans, construct a polar attachment organelle (AO) that is used for both adherence to host cells and gliding motility. However, the irregular phylogenetic distribution of similar structures within the mycoplasmas, as well as compositional and ultrastructural differences among these AOs, suggests that AOs have arisen several times through convergent evolution. We investigated the ultrastructure and protein composition of the cytoskeleton-like material of the M. penetrans AO with several forms of microscopy and biochemical analysis, to determine whether the M. penetrans AO was constructed at the molecular level on principles similar to those of other mycoplasmas, such as Mycoplasma pneumoniae and Mycoplasma mobile We found that the M. penetrans AO interior was generally dissimilar from that of other mycoplasmas, in that it exhibited considerable heterogeneity in size and shape, suggesting a gel-like nature. In contrast, several of the 12 potential protein components identified by mass spectrometry of M. penetrans detergent-insoluble proteins shared certain distinctive biochemical characteristics with M. pneumoniae AO proteins, although not with M. mobile proteins. We conclude that convergence between M. penetrans and M. pneumoniae AOs extends to the molecular level, leading to the possibility that the less organized material in both M. pneumoniae and M. penetrans is the substance principally responsible for the organization and function of the AO.IMPORTANCEMycoplasma penetrans is a bacterium that infects HIV-positive patients and may contribute to the progression of AIDS. It attaches to host cells through a structure called an AO, but it is not clear how it builds this structure. Our research is significant not only because it identifies the novel protein components that make up the material within the AO that give it its structure but also because we find that the M. penetrans AO is organized unlike AOs from other mycoplasmas, suggesting that similar structures have evolved multiple times. From this work, we derive some basic principles by which mycoplasmas, and potentially all organisms, build structures at the subcellular level.
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Zafrir Z, Tuller T. Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. BMC Bioinformatics 2017; 18:77. [PMID: 28143396 PMCID: PMC5286865 DOI: 10.1186/s12859-017-1497-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/27/2017] [Indexed: 12/30/2022] Open
Abstract
Background The regulation of all gene expression steps (e.g., Transcription, RNA processing, Translation, and mRNA Degradation) is known to be primarily encoded in different parts of genes and in genomic regions in proximity to genes (e.g., promoters, untranslated regions, coding regions, introns, etc.). However, the entire gene expression codes and the genomic regions where they are encoded are still unknown. Results Here, we employ an unsupervised approach to estimate the concentration of gene expression codes in different non-coding parts of genes and transcripts, such as introns and untranslated regions, focusing on three model organisms (Escherichia coli, Saccharomyces cerevisiae, and Schizosaccharomyces pombe). Our analyses support the conjecture that regions adjacent to the beginning and end of ORFs and the beginning and end of introns tend to include higher concentration of gene expression information relatively to regions further away. In addition, we report the exact regions with elevated concentration of gene expression codes. Furthermore, we demonstrate that the concentration of these codes in different genetic regions is correlated with the expression levels of the corresponding genes, and with splicing efficiency measurements and meiotic stage gene expression measurements in S. cerevisiae. Conclusion We suggest that these discoveries improve our understanding of gene expression regulation and evolution; they can also be used for developing improved models of genome/gene evolution and for engineering gene expression in various biotechnological and synthetic biology applications. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1497-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zohar Zafrir
- Department of Biomedical Engineering, Tel Aviv University, P.O. Box 39040, Tel Aviv, 6997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, P.O. Box 39040, Tel Aviv, 6997801, Israel. .,Sagol School of Neuroscience, Tel Aviv University, P.O. Box 39040, Tel Aviv, 6997801, Israel.
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Seward EA, Kelly S. Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms. Genome Biol 2016; 17:226. [PMID: 27842572 PMCID: PMC5109750 DOI: 10.1186/s13059-016-1087-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/12/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Genomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism's environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms. However, the impact of the relative availability of dietary nitrogen on genome composition and codon bias is poorly understood. RESULTS Here we show that differential nitrogen availability, due to differences in environment and dietary inputs, is a major determinant of genome nucleotide composition and synonymous codon use in both bacterial and eukaryotic microorganisms. Specifically, low nitrogen availability species use nucleotides that require fewer nitrogen atoms to encode the same genes compared to high nitrogen availability species. Furthermore, we provide a novel selection-mutation framework for the evaluation of the impact of metabolism on gene sequence evolution and show that it is possible to predict the metabolic inputs of related organisms from an analysis of the raw nucleotide sequence of their genes. CONCLUSIONS Taken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environments.
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Affiliation(s)
- Emily A Seward
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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Shimizu T. Inflammation-inducing Factors of Mycoplasma pneumoniae. Front Microbiol 2016; 7:414. [PMID: 27065977 PMCID: PMC4814563 DOI: 10.3389/fmicb.2016.00414] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/14/2016] [Indexed: 12/17/2022] Open
Abstract
Mycoplasma pneumoniae, which causes mycoplasmal pneumonia in human, mainly causes pneumonia in children, although it occasionally causes disease in infants and geriatrics. Some pathogenic factors produced by M. pneumoniae, such as hydrogen peroxide and Community-Acquired Respiratory Distress Syndrome (CARDS) toxin have been well studied. However, these factors alone cannot explain this predilection. The low incidence rate of mycoplasmal pneumonia in infants and geriatrics implies that the strong inflammatory responses induced by M. pneumoniae coordinate with the pathogenic factors to induce pneumonia. However, M. pneumoniae lacks a cell wall and does not possess an inflammation-inducing endotoxin, such as lipopolysaccharide (LPS). In M. pneumoniae, lipoproteins were identified as an inflammation-inducing factor. Lipoproteins induce inflammatory responses through Toll-like receptors (TLR) 2. Because Mycoplasma species lack a cell wall and lipoproteins anchored in the membrane are exposed, lipoproteins and TLR2 have been thought to be important for the pathogenesis of M. pneumoniae. However, recent reports suggest that M. pneumoniae also induces inflammatory responses also in a TLR2-independent manner. TLR4 and autophagy are involved in this TLR2-independent inflammation. In addition, the CARDS toxin or M. pneumoniae cytadherence induces inflammatory responses through an intracellular receptor protein complex called the inflammasome. In this review, the inflammation-inducing factors of M. pneumoniae are summarized.
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Affiliation(s)
- Takashi Shimizu
- Laboratory of Veterinary Public Health, Joint Faculty of Veterinary Medicine, Yamaguchi University Yamaguchi, Japan
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Yacoub E, Ben Abdelmoumen Mardassi B. Mm19, a Mycoplasma meleagridis Major Surface Nuclease that Is Related to the RE_AlwI Superfamily of Endonucleases. PLoS One 2016; 11:e0152171. [PMID: 27010566 PMCID: PMC4807054 DOI: 10.1371/journal.pone.0152171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/09/2016] [Indexed: 11/19/2022] Open
Abstract
Mycoplasma meleagridis infection is widespread in turkeys, causing poor growth and feathering, airsacculitis, osteodystrophy, and reduction in hatchability. Like most mycoplasma species, M. meleagridis is characterized by its inability to synthesize purine and pyrimidine nucleotides de novo. Consistent with this intrinsic deficiency, we here report the cloning, expression, and characterization of a M. meleagridis gene sequence encoding a major surface nuclease, referred to as Mm19. Mm19 consists of a 1941-bp ORF encoding a 646-amino-acid polypeptide with a predicted molecular mass of 74,825 kDa. BLASTP analysis revealed a significant match with the catalytic/dimerization domain of type II restriction enzymes of the RE_AlwI superfamily. This finding is consistent with the genomic location of Mm19 sequence, which dispalys characteristics of a typical type II restriction-modification locus. Like intact M. meleagridis cells, the E. coli-expressed Mm19 fusion product was found to exhibit a nuclease activity against plasmid DNA, double-stranded DNA, single-stranded DNA, and RNA. The Mm19-associated nuclease activity was consistently enhanced with Mg2+ divalent cations, a hallmark of type II restriction enzymes. A rabbit hyperimmune antiserum raised against the bacterially expressed Mm19 strongly reacted with M. meleagridis intact cells and fully neutralized the surface-bound nuclease activity. Collectively, the results show that M. meleagridis expresses a strong surface-bound nuclease activity, which is the product of a single gene sequence that is related to the RE_AlwI superfamily of endonucleases.
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Affiliation(s)
- Elhem Yacoub
- Unit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Institut Pasteur de Tunis, University of Tunis, El Manar, Tunisia
| | - Boutheina Ben Abdelmoumen Mardassi
- Unit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Institut Pasteur de Tunis, University of Tunis, El Manar, Tunisia
- * E-mail:
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Tatarinova TV, Lysnyansky I, Nikolsky YV, Bolshoy A. The mysterious orphans of Mycoplasmataceae. Biol Direct 2016; 11:2. [PMID: 26747447 PMCID: PMC4706650 DOI: 10.1186/s13062-015-0104-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/30/2015] [Indexed: 01/08/2023] Open
Abstract
Background The length of a protein sequence is largely determined by its function. In certain species, it may be also affected by additional factors, such as growth temperature or acidity. In 2002, it was shown that in the bacterium Escherichia coli and in the archaeon Archaeoglobus fulgidus, protein sequences with no homologs were, on average, shorter than those with homologs (BMC Evol Biol 2:20, 2002). It is now generally accepted that in bacterial and archaeal genomes the distributions of protein length are different between sequences with and without homologs. In this study, we examine this postulate by conducting a comprehensive analysis of all annotated prokaryotic genomes and by focusing on certain exceptions. Results We compared the distribution of lengths of “having homologs proteins” (HHPs) and “non-having homologs proteins” (orphans or ORFans) in all currently completely sequenced and COG-annotated prokaryotic genomes. As expected, the HHPs and ORFans have strikingly different length distributions in almost all genomes. As previously established, the HHPs, indeed are, on average, longer than the ORFans, and the length distributions for the ORFans have a relatively narrow peak, in contrast to the HHPs, whose lengths spread over a wider range of values. However, about thirty genomes do not obey these rules. Practically all genomes of Mycoplasma and Ureaplasma have atypical ORFans distributions, with the mean lengths of ORFan larger than the mean lengths of HHPs. These genera constitute over 80 % of atypical genomes. Conclusions We confirmed on a ubiquitous set of genomes that the previous observation of HHPs and ORFans have different gene length distributions. We also showed that Mycoplasmataceae genomes have very distinctive distributions of ORFans lengths. We offer several possible biological explanations of this phenomenon, such as an adaptation to Mycoplasmataceae’s ecological niche, specifically its “quiet” co-existence with host organisms, resulting in long ABC transporters. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0104-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tatiana V Tatarinova
- Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, 90027, CA, USA. .,Spatial Sciences Institute, University of Southern California, Los Angeles, 90089, CA, USA.
| | - Inna Lysnyansky
- Mycoplasma Unit, Division of Avian and Aquatic Diseases, Kimron Veterinary Institute, POB 12, Beit Dagan, 50250, Israel.
| | - Yuri V Nikolsky
- School of Systems Biology, George Mason University, 10900 University Blvd, MSN 5B3, Manassas, VA, 20110, USA. .,Prosapia Genetics, LLC, 534 San Andres Dr., Solana Beach, CA, 92075, USA. .,Vavilov Institute of General Genetics, Moscow, Russian Federation.
| | - Alexander Bolshoy
- Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, Haifa, Israel.
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Klubal R, Kopecky J, Nesvorna M, Sparagano OAE, Thomayerova J, Hubert J. Prevalence of pathogenic bacteria in Ixodes ricinus ticks in Central Bohemia. EXPERIMENTAL & APPLIED ACAROLOGY 2016; 68:127-137. [PMID: 26612395 DOI: 10.1007/s10493-015-9988-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/31/2015] [Indexed: 06/05/2023]
Abstract
Bacteria associated with the tick Ixodes ricinus were assessed in specimens unattached or attached to the skin of cats, dogs and humans, collected in the Czech Republic. The bacteria were detected by PCR in 97 of 142 pooled samples including 204 ticks, i.e. 1-7 ticks per sample, collected at the same time from one host. A fragment of the bacterial 16S rRNA gene was amplified, cloned and sequenced from 32 randomly selected samples. The most frequent sequences were those related to Candidatus Midichloria midichlori (71% of cloned sequences), followed by Diplorickettsia (13%), Spiroplasma (3%), Rickettsia (3%), Pasteurella (3%), Morganella (3%), Pseudomonas (2%), Bacillus (1%), Methylobacterium (1%) and Phyllobacterium (1%). The phylogenetic analysis of Spiroplasma 16S rRNA gene sequences showed two groups related to Spiroplasma eriocheiris and Spiroplasma melliferum, respectively. Using group-specific primers, the following potentially pathogenic bacteria were detected: Borellia (in 20% of the 142 samples), Rickettsia (12%), Spiroplasma (5%), Diplorickettsia (5%) and Anaplasma (2%). In total, 68% of I. ricinus samples (97/142) contained detectable bacteria and 13% contained two or more putative pathogenic groups. The prevalence of tick-borne bacteria was similar to the observations in other European countries.
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Affiliation(s)
| | - Jan Kopecky
- Crop Research Institute, Drnovska 507/73, Ruzyne, 16106, Prague 6, Czech Republic
| | - Marta Nesvorna
- Crop Research Institute, Drnovska 507/73, Ruzyne, 16106, Prague 6, Czech Republic
| | | | | | - Jan Hubert
- Medical Centre Prague, Prague, Czech Republic.
- Crop Research Institute, Drnovska 507/73, Ruzyne, 16106, Prague 6, Czech Republic.
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Niller HH, Minarovits J. Patho-epigenetics of Infectious Diseases Caused by Intracellular Bacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 879:107-130. [PMID: 26659266 DOI: 10.1007/978-3-319-24738-0_6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In multicellular eukaryotes including plants, animals and humans, epigenetic reprogramming may play a role in the pathogenesis of a wide variety of diseases. Recent studies revealed that in addition to viruses, pathogenic bacteria are also capable to dysregulate the epigenetic machinery of their target cells. In this chapter we focus on epigenetic alterations induced by bacteria infecting humans. Most of them are obligate or facultative intracellular bacteria that produce either bacterial toxins and surface proteins targeting the host cell membrane, or synthesise effector proteins entering the host cell nucleus. These bacterial products typically elicit histone modifications, i.e. alter the "histone code". Bacterial pathogens are capable to induce alterations of host cell DNA methylation patterns, too. Such changes in the host cell epigenotype and gene expression pattern may hinder the antibacterial immune response and create favourable conditions for bacterial colonization, growth, or spread. Epigenetic dysregulation mediated by bacterial products may also facilitate the production of inflammatory cytokines and other inflammatory mediators affecting the epigenotype of their target cells. Such indirect epigenetic changes as well as direct interference with the epigenetic machinery of the host cells may contribute to the initiation and progression of malignant tumors associated with distinct bacterial infections.
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Affiliation(s)
- Hans Helmut Niller
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Janos Minarovits
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, Tisza Lajos krt. 64, H-6720, Szeged, Hungary.
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Hanajima D, Aoyagi T, Hori T. Survival of free-living Acholeplasma in aerated pig manure slurry revealed by (13)C-labeled bacterial biomass probing. Front Microbiol 2015; 6:1206. [PMID: 26583009 PMCID: PMC4628116 DOI: 10.3389/fmicb.2015.01206] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 10/16/2015] [Indexed: 12/02/2022] Open
Abstract
Many studies have been performed on microbial community succession and/or predominant taxa during the composting process; however, the ecophysiological roles of microorganisms are not well understood because microbial community structures are highly diverse and dynamic. Bacteria are the most important contributors to the organic-waste decomposition process, while decayed bacterial cells can serve as readily digested substrates for other microbial populations. In this study, we investigated the active bacterial species responsible for the assimilation of dead bacterial cells and their components in aerated pig manure slurry by using 13C-labeled bacterial biomass probing. After 3 days of forced aeration, 13C-labeled and unlabeled dead Escherichia coli cell suspensions were added to the slurry. The suspensions contained 13C-labeled and unlabeled bacterial cell components, possibly including the cell wall and membrane, as well as intracellular materials. RNA extracted from each slurry sample 2 h after addition of E. coli suspension was density-resolved by isopycnic centrifugation and analyzed by terminal restriction fragment length polymorphism, followed by cloning and sequencing of bacterial 16S rRNA genes. In the heavy isotopically labeled RNA fraction, the predominant 13C-assimilating population was identified as belonging to the genus Acholeplasma, which was not detected in control heavy RNA. Acholeplasma spp. have limited biosynthetic capabilities and possess a wide variety of transporters, resulting in their metabolic dependence on external carbon and energy sources. The prevalence of Acholeplasma spp. was further confirmed in aerated pig manure slurry from four different pig farms by pyrosequencing of 16S rRNA genes; their relative abundance was ∼4.4%. Free-living Acholeplasma spp. had a competitive advantage for utilizing dead bacterial cells and their components more rapidly relative to other microbial populations, thus allowing the survival and prevalence of Acholeplasma spp. in pig manure slurry.
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Affiliation(s)
- Dai Hanajima
- Dairy Research Division, Hokkaido Agricultural Research Center, National Agricultural and Food Research Organization Sapporo, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
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Bakhshi A, Safari M, Erami M, Kheirkhah B, Pourbakhsh A, Pourbabei H. Sequences of Mycoplasma hominis in Patients with Urinary Tract Infection in a Hospital in Kashan, Iran. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/jm.2015.260.269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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35
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Sharma S, Tivendale KA, Markham PF, Browning GF. Disruption of the membrane nuclease gene (MBOVPG45_0215) of Mycoplasma bovis greatly reduces cellular nuclease activity. J Bacteriol 2015; 197:1549-58. [PMID: 25691526 PMCID: PMC4403647 DOI: 10.1128/jb.00034-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 02/06/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Although the complete genome sequences of three strains of Mycoplasma bovis are available, few studies have examined gene function in this important pathogen. Mycoplasmas lack the biosynthetic machinery for the de novo synthesis of nucleic acid precursors, so nucleases are likely to be essential for them to acquire nucleotide precursors. Three putative membrane nucleases have been annotated in the genome of M. bovis strain PG45, MBOVPG45_0089 and MBOVPG45_0310, both of which have the thermonuclease (TNASE_3) functional domain, and MBOVPG45_0215 (mnuA), which has an exonuclease/endonuclease/phosphatase domain. While previous studies have demonstrated the function of TNASE_3 domain nucleases in several mycoplasmas, quantitative comparisons of the contributions of different nucleases to cellular nuclease activity have been lacking. Mapping of a library of 319 transposon mutants of M. bovis PG45 by direct genome sequencing identified mutants with insertions in MBOVPG45_0310 (the Δ0310 mutant) and MBOVPG45_0215 (the Δ0215 mutant). In this study, the detection of the product of MBOVPG45_0215 in the Triton X-114 fraction of M. bovis cell lysates, its cell surface exposure, and its predicted signal peptide suggested that it is a surface-exposed lipoprotein nuclease. Comparison of a ΔmnuA mutant with wild-type M. bovis on native and denatured DNA gels and in digestion assays using double-stranded phage λ DNA and closed circular plasmid DNA demonstrated that inactivation of this gene abolishes most of the cellular exonuclease and endonuclease activity of M. bovis. This activity could be fully restored by complementation with the wild-type mnuA gene, demonstrating that MnuA is the major cellular nuclease of M. bovis. IMPORTANCE Nucleases are thought to be important contributors to virulence and crucial for the maintenance of a nutritional supply of nucleotides in mycoplasmas that are pathogenic in animals. This study demonstrates for the first time that of the three annotated cell surface nuclease genes in an important pathogenic mycoplasma, the homologue of the thermostable nuclease identified in Gram-positive bacteria is responsible for the majority of the nuclease activity detectable in vitro.
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Affiliation(s)
- Shukriti Sharma
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Kelly A Tivendale
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Philip F Markham
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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Vujanovic L, Shi J, Kirkwood JM, Storkus WJ, Butterfield LH. Molecular mimicry of MAGE-A6 and Mycoplasma penetrans HF-2 epitopes in the induction of antitumor CD8 + T-cell responses. Oncoimmunology 2014; 3:e954501. [PMID: 25960935 DOI: 10.4161/21624011.2014.954501] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/11/2014] [Indexed: 11/19/2022] Open
Abstract
A promising vaccine strategy for the treatment of cancer involves the use of vaccines incorporating tumor antigen-derived synthetic peptides that can be coordinately recognized by specific CD4+ and CD8+ T-cells. Previously, we reported that a MAGE-A6-derived peptide (MAGE-A6172-187) and its highly-immunogenic and cross-reactive homolog derived from Mycoplasma penetrans HF-2 permease (HF-2216-229) are promiscuously presented by multiple HLA-DR alleles to responder CD4+ T-cells obtained from healthy donors and melanoma patients. Here, we investigated whether these same peptides could concomitantly stimulate cross-reactive MAGE-A6-specific CD8+ T-cell responses in vitro using cells isolated from HLA-A*0201 (HLA-A2)+ healthy individuals and patients with melanoma. We now show that MAGE-A6172-187 and, even more so, HF-2216-229, induce memory CD8+ T cells that recognize HLA-A2+ MAGE-A6+ tumor target cells. The immunogenicity of these peptides was at least partially attributed to their embedded MAGE-A6176-185 and HF-2220-229 "homologous" sequences. The functional avidity of HF-2216-229 peptide-primed CD8+ T cells for the MAGE-A6172-187 peptide was more than 100-fold greater than that of CD8+ T cells primed with the corresponding MAGE-A6 peptide. Additionally, these 2 peptides were recognized in interferon γ (IFNγ) and granzyme B ELISPOT assays by CD8+ T-cell clones displaying variable T-cell receptor (TCR) Vβ usage. These data suggest that the immune cross-reactivity of the MAGE-A6172-187 and HF-2216-229 peptides extends to CD8+ T cells, at least in HLA-A2+ donors, and supports the potential translational utility of these epitopes in clinical vaccine formulations and for immunomonitoring of cancer patients.
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Key Words
- APC, antigen presenting cell
- AdV, recombinant adenoviral vector
- CD8+ T-cell
- CTL, cytotoxic T lymphocyte
- EBV, Epstein-Barr virus
- FBS, fetal bovine serum
- HD, healthy donor
- HLA, human leukocyte antigen
- HPLC, high-performance liquid chromatography
- IVS, in vitro stimulation
- MACS, Magnetic-Activated Cell Sorting
- MAGE-A6
- MOI, multiplicity of infection
- Mycoplasma penetrans
- PBMC, peripheral blood mononuclear cell
- PFU, plaque forming units
- RT-PCR, reverse transcription polymerase chain reaction
- TAA, tumor associated antigen
- TCM, T cell media
- TCR, T-cell receptor
- epitope mimic
- iDC, immature dendritic cells
- mDC, mature dendritic cells
- melanoma
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Affiliation(s)
- Lazar Vujanovic
- University of Pittsburgh Cancer Institute ; Pittsburgh, PA USA ; University of Pittsburgh School of Medicine; Department of Medicine ; Pittsburgh, PA USA
| | - Jian Shi
- University of Pittsburgh Cancer Institute ; Pittsburgh, PA USA ; University of Pittsburgh School of Medicine; Department of Medicine ; Pittsburgh, PA USA
| | - John M Kirkwood
- University of Pittsburgh Cancer Institute ; Pittsburgh, PA USA ; University of Pittsburgh School of Medicine; Department of Medicine ; Pittsburgh, PA USA
| | - Walter J Storkus
- University of Pittsburgh Cancer Institute ; Pittsburgh, PA USA ; University of Pittsburgh School of Medicine; Department of Immunology ; Pittsburgh, PA USA ; University of Pittsburgh School of Medicine; Department of Dermatology ; Pittsburgh, PA USA
| | - Lisa H Butterfield
- University of Pittsburgh Cancer Institute ; Pittsburgh, PA USA ; University of Pittsburgh School of Medicine; Department of Medicine ; Pittsburgh, PA USA ; University of Pittsburgh School of Medicine; Department of Immunology ; Pittsburgh, PA USA ; University of Pittsburgh School of Medicine; Department of Surgery ; Pittsburgh, PA USA
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Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. BMC Genomics 2014; 15:374. [PMID: 24885563 PMCID: PMC4035089 DOI: 10.1186/1471-2164-15-374] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 05/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nucleomorphs are residual nuclei derived from eukaryotic endosymbionts in chlorarachniophyte and cryptophyte algae. The endosymbionts that gave rise to nucleomorphs and plastids in these two algal groups were green and red algae, respectively. Despite their independent origin, the chlorarachniophyte and cryptophyte nucleomorph genomes share similar genomic features such as extreme size reduction and a three-chromosome architecture. This suggests that similar reductive evolutionary forces have acted to shape the nucleomorph genomes in the two groups. Thus far, however, only a single chlorarachniophyte nucleomorph and plastid genome has been sequenced, making broad evolutionary inferences within the chlorarachniophytes and between chlorarachniophytes and cryptophytes difficult. We have sequenced the nucleomorph and plastid genomes of the chlorarachniophyte Lotharella oceanica in order to gain insight into nucleomorph and plastid genome diversity and evolution. RESULTS The L. oceanica nucleomorph genome was found to consist of three linear chromosomes totaling ~610 kilobase pairs (kbp), much larger than the 373 kbp nucleomorph genome of the model chlorarachniophyte Bigelowiella natans. The L. oceanica plastid genome is 71 kbp in size, similar to that of B. natans. Unexpectedly long (~35 kbp) sub-telomeric repeat regions were identified in the L. oceanica nucleomorph genome; internal multi-copy regions were also detected. Gene content analyses revealed that nucleomorph house-keeping genes and spliceosomal intron positions are well conserved between the L. oceanica and B. natans nucleomorph genomes. More broadly, gene retention patterns were found to be similar between nucleomorph genomes in chlorarachniophytes and cryptophytes. Chlorarachniophyte plastid genomes showed near identical protein coding gene complements as well as a high level of synteny. CONCLUSIONS We have provided insight into the process of nucleomorph genome evolution by elucidating the fine-scale dynamics of sub-telomeric repeat regions. Homologous recombination at the chromosome ends appears to be frequent, serving to expand and contract nucleomorph genome size. The main factor influencing nucleomorph genome size variation between different chlorarachniophyte species appears to be expansion-contraction of these telomere-associated repeats rather than changes in the number of unique protein coding genes. The dynamic nature of chlorarachniophyte nucleomorph genomes lies in stark contrast to their plastid genomes, which appear to be highly stable in terms of gene content and synteny.
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Vande Voorde J, Balzarini J, Liekens S. Mycoplasmas and cancer: focus on nucleoside metabolism. EXCLI JOURNAL 2014; 13:300-22. [PMID: 26417262 PMCID: PMC4464442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 02/19/2014] [Indexed: 11/26/2022]
Abstract
The standard of care for patients suffering cancer often includes treatment with nucleoside analogues (NAs). NAs are internalized by cell-specific nucleobase/nucleoside transporters and, after enzymatic activation (often one or more phosphorylation steps), interfere with cellular nucleo(s)(t)ide metabolism and DNA/RNA synthesis. Therefore, their efficacy is highly dependent on the expression and activity of nucleo(s)(t)ide-metabolizing enzymes, and alterations thereof (e.g. by down/upregulated expression or mutations) may change the susceptibility to NA-based therapy and/or confer drug resistance. Apart from host cell factors, several other variables including microbial presence may determine the metabolome (i.e. metabolite concentrations) of human tissues. Studying the diversity of microorganisms that are associated with the human body has already provided new insights in several diseases (e.g. diabetes and inflammatory bowel disease) and the metabolic exchange between tissues and their specific microbiota was found to affect the bioavailability and toxicity of certain anticancer drugs, including NAs. Several studies report a preferential colonization of tumor tissues with some mycoplasma species (mostly Mycoplasma hyorhinis). These prokaryotes are also a common source of cell culture contamination and alter the cytostatic activity of some NAs in vitro due to the expression of nucleoside-catabolizing enzymes. Mycoplasma infection may therefore bias experimental work with NAs, and their presence in the tumor microenvironment could be of significance when optimizing nucleoside-based cancer treatment.
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Affiliation(s)
- Johan Vande Voorde
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, blok x - bus 1030, B-3000 Leuven, Belgium
| | - Jan Balzarini
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, blok x - bus 1030, B-3000 Leuven, Belgium
| | - Sandra Liekens
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, blok x - bus 1030, B-3000 Leuven, Belgium
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Vishnyakov IE, Borchsenius SN. Mycoplasma heat shock proteins and their genes. Microbiology (Reading) 2014. [DOI: 10.1134/s002626171306012x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Lo WS, Ku C, Chen LL, Chang TH, Kuo CH. Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. Genome Biol Evol 2013; 5:1512-23. [PMID: 23873917 PMCID: PMC3762197 DOI: 10.1093/gbe/evt108] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Mosquitoes are hosts of several Spiroplasma species that belong to different serogroups. To investigate the genetic mechanisms that may be involved in the utilization of similar hosts in these phylogenetically distinct bacteria, we determined the complete genome sequences of Spiroplasma diminutum and S. taiwanense for comparative analysis. The genome alignment indicates that their chromosomal organization is highly conserved, which is in sharp contrast to the elevated genome instabilities observed in other Spiroplasma lineages. Examination of the substrate utilization strategies revealed that S. diminutum can use a wide range of carbohydrates, suggesting that it is well suited to living in the gut (and possibly the circulatory system) of its mosquito hosts. In comparison, S. taiwanense has lost several carbohydrate utilization genes and acquired additional sets of oligopeptide transporter genes through tandem duplications, suggesting that proteins from digested blood meal or lysed host cells may be an important nutrient source. Moreover, one glycerol-3-phosphate oxidase gene (glpO) was found in S. taiwanense but not S. diminutum. This gene is linked to the production of reactive oxygen species and has been shown to be a major virulence factor in Mycoplasma mycoides. This finding may explain the pathogenicity of S. taiwanense observed in previous artificial infection experiments, while no apparent effect was found for S. diminutum. To infer the gene content evolution at deeper divergence levels, we incorporated other Mollicutes genomes for comparative analyses. The results suggest that the losses of biosynthetic pathways are a recurrent theme in these host-associated bacteria.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Tanifuji G, Onodera NT, Moore CE, Archibald JM. Reduced Nuclear Genomes Maintain High Gene Transcription Levels. Mol Biol Evol 2013; 31:625-35. [DOI: 10.1093/molbev/mst254] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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Reconstitution of an active arginine deiminase pathway in Mycoplasma pneumoniae M129. Infect Immun 2013; 81:3742-9. [PMID: 23897620 DOI: 10.1128/iai.00441-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some species of the genus Mycoplasma code for the arginine deiminase pathway (ADI), which enables these bacteria to produce ATP from arginine by the successive reaction of three enzymes: arginine deiminase (ArcA), ornithine carbamoyltransferase (ArcB), and carbamate kinase (ArcC). It so far appears that independently isolated strains of Mycoplasma pneumoniae encode an almost identical truncated version of the ADI pathway in which the proteins ArcA and ArcB have lost their original enzymatic activities due to the deletion of significant regions of these proteins. To study the consequences of a functional ADI pathway, M. pneumoniae M129 was successfully transformed with the cloned functional arcA, arcB, and arcC genes from Mycoplasma fermentans. Enzymatic tests showed that while the M. pneumoniae ArcAB and ArcABC transformants possess functional arginine deiminase, ornithine carbamoyltransferase, and carbamate kinase, they were unable to grow on arginine as the sole energy source. Nevertheless, infection of a lung epithelial cell line, A549, with the M. pneumoniae transformants showed that almost 100% of the infected host cells were nonviable, while most of the lung cells infected with nontransformed M. pneumoniae were viable under the same experimental conditions.
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Jones TE, Ribas de Pouplana L, Alexander RW. Evidence for late resolution of the aux codon box in evolution. J Biol Chem 2013; 288:19625-32. [PMID: 23696642 DOI: 10.1074/jbc.m112.449249] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Recognition strategies for tRNA aminoacylation are ancient and highly conserved, having been selected very early in the evolution of the genetic code. In most cases, the trinucleotide anticodons of tRNA are important identity determinants for aminoacylation by cognate aminoacyl-tRNA synthetases. However, a degree of ambiguity exists in the recognition of certain tRNA(Ile) isoacceptors that are initially transcribed with the methionine-specifying CAU anticodon. In most organisms, the C34 wobble position in these tRNA(Ile) precursors is rapidly modified to lysidine to prevent recognition by methionyl-tRNA synthetase (MRS) and production of a chimeric Met-tRNA(Ile) that would compromise translational fidelity. In certain bacteria, however, lysidine modification is not required for MRS rejection, indicating that this recognition strategy is not universally conserved and may be relatively recent. To explore the actual distribution of lysidine-dependent tRNA(Ile) rejection by MRS, we have investigated the ability of bacterial MRSs from different clades to differentiate cognate tRNACAU(Met) from near-cognate tRNACAU(Ile). Discrimination abilities vary greatly and appear unrelated to phylogenetic or structural features of the enzymes or sequence determinants of the tRNA. Our data indicate that tRNA(Ile) identity elements were established late and independently in different bacterial groups. We propose that the observed variation in MRS discrimination ability reflects differences in the evolution of genetic code machineries of emerging bacterial clades.
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Affiliation(s)
- Thomas E Jones
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109-7486, USA
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Cacciotto C, Addis MF, Coradduzza E, Carcangiu L, Nuvoli AM, Tore G, Dore GM, Pagnozzi D, Uzzau S, Chessa B, Pittau M, Alberti A. Mycoplasma agalactiae MAG_5040 is a Mg2+-dependent, sugar-nonspecific SNase recognised by the host humoral response during natural infection. PLoS One 2013; 8:e57775. [PMID: 23469065 PMCID: PMC3585158 DOI: 10.1371/journal.pone.0057775] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 01/25/2013] [Indexed: 11/18/2022] Open
Abstract
In this study the enzymatic activity of Mycoplasma agalactiae MAG_5040, a magnesium-dependent nuclease homologue to the staphylococcal SNase was characterized and its antigenicity during natural infections was established. A UGA corrected version of MAG_5040, lacking the region encoding the signal peptide, was expressed in Escherichia coli as a GST fusion protein. Recombinant GST-MAG_5040 exhibits nuclease activity similar to typical sugar-nonspecific endo- and exonucleases, with DNA as the preferred substrate and optimal activity in the presence of 20 mM MgCl2 at temperatures ranging from 37 to 45°C. According to in silico analyses, the position of the gene encoding MAG_5040 is consistently located upstream an ABC transporter, in most sequenced mycoplasmas belonging to the Mycoplasma hominis group. In M. agalactiae, MAG_5040 is transcribed in a polycistronic RNA together with the ABC transporter components and with MAG_5030, which is predicted to be a sugar solute binding protein by 3D modeling and homology search. In a natural model of sheep and goats infection, anti-MAG_5040 antibodies were detected up to 9 months post infection. Taking into account its enzymatic activity, MAG_5040 could play a key role in Mycoplasma agalactiae survival into the host, contributing to host pathogenicity. The identification of MAG_5040 opens new perspectives for the development of suitable tools for the control of contagious agalactia in small ruminants.
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Affiliation(s)
- Carla Cacciotto
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | | | - Elisabetta Coradduzza
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Laura Carcangiu
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Anna Maria Nuvoli
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Gessica Tore
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Gian Mario Dore
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | | | - Sergio Uzzau
- Porto Conte Ricerche Srl, Tramariglio, Alghero (SS), Italy
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Bernardo Chessa
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Marco Pittau
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
| | - Alberto Alberti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Sassari, Italy
- * E-mail:
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Lo WS, Chen LL, Chung WC, Gasparich GE, Kuo CH. Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium. BMC Genomics 2013; 14:22. [PMID: 23324436 PMCID: PMC3563533 DOI: 10.1186/1471-2164-14-22] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 12/20/2012] [Indexed: 11/17/2022] Open
Abstract
Background The genus Spiroplasma contains a group of helical, motile, and wall-less bacteria in the class Mollicutes. Similar to other members of this class, such as the animal-pathogenic Mycoplasma and the plant-pathogenic ‘Candidatus Phytoplasma’, all characterized Spiroplasma species were found to be associated with eukaryotic hosts. While most of the Spiroplasma species appeared to be harmless commensals of insects, a small number of species have evolved pathogenicity toward various arthropods and plants. In this study, we isolated a novel strain of honeybee-associated S. melliferum and investigated its genetic composition and evolutionary history by whole-genome shotgun sequencing and comparative analysis with other Mollicutes genomes. Results The whole-genome shotgun sequencing of S. melliferum IPMB4A produced a draft assembly that was ~1.1 Mb in size and covered ~80% of the chromosome. Similar to other Spiroplasma genomes that have been studied to date, we found that this genome contains abundant repetitive sequences that originated from plectrovirus insertions. These phage fragments represented a major obstacle in obtaining a complete genome sequence of Spiroplasma with the current sequencing technology. Comparative analysis of S. melliferum IPMB4A with other Spiroplasma genomes revealed that these phages may have facilitated extensive genome rearrangements in these bacteria and contributed to horizontal gene transfers that led to species-specific adaptation to different eukaryotic hosts. In addition, comparison of gene content with other Mollicutes suggested that the common ancestor of the SEM (Spiroplasma, Entomoplasma, and Mycoplasma) clade may have had a relatively large genome and flexible metabolic capacity; the extremely reduced genomes of present day Mycoplasma and ‘Candidatus Phytoplasma’ species are likely to be the result of independent gene losses in these lineages. Conclusions The findings in this study highlighted the significance of phage insertions and horizontal gene transfer in the evolution of bacterial genomes and acquisition of pathogenicity. Furthermore, the inclusion of Spiroplasma in comparative analysis has improved our understanding of genome evolution in Mollicutes. Future improvements in the taxon sampling of available genome sequences in this group are required to provide further insights into the evolution of these important pathogens of humans, animals, and plants.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI. Proc Natl Acad Sci U S A 2012; 110:105-10. [PMID: 23248272 DOI: 10.1073/pnas.1207986110] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cytosine methylation promotes deamination. In eukaryotes, CpG methylation is thought to account for CpG underrepresentation. Whether scarcity of CpGs in prokaryotic genomes is diagnostic for methylation is not clear. Here, we report that Mycoplasms tend to be CpG depleted and to harbor a family of constitutively expressed or phase variable CpG-specific DNA methyltransferases. The very CpG poor Mycoplasma penetrans and its constitutively active CpG-specific methyltransferase M.MpeI were chosen for further characterization. Genome-wide sequencing of bisulfite-converted DNA indicated that M.MpeI methylated CpG target sites both in vivo and in vitro in a locus-nonselective manner. A crystal structure of M.MpeI with DNA at 2.15-Å resolution showed that the substrate base was flipped and that its place in the DNA stack was taken by a glutamine residue. A phenylalanine residue was intercalated into the "weak" CpG step of the nonsubstrate strand, indicating mechanistic similarities in the recognition of the short CpG target sequence by prokaryotic and eukaryotic DNA methyltransferases.
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47
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Jurkovic DA, Hughes MR, Balish MF. Analysis of energy sources for Mycoplasma penetrans gliding motility. FEMS Microbiol Lett 2012; 338:39-45. [PMID: 23066969 DOI: 10.1111/1574-6968.12026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/08/2012] [Accepted: 10/08/2012] [Indexed: 11/30/2022] Open
Abstract
Mycoplasma penetrans, a potential human pathogen found mainly in HIV-infected individuals, uses a tip structure for both adherence and gliding motility. To improve our understanding of the molecular mechanism of M. penetrans gliding motility, we used chemical inhibitors of energy sources associated with motility of other organisms to determine which of these is used by M. penetrans and also tested whether gliding speed responded to temperature and pH. Mycoplasma penetrans gliding motility was not eliminated in the presence of a proton motive force inhibitor, a sodium motive force inhibitor, or an agent that depletes cellular ATP. At near-neutral pH, gliding speed increased as temperature increased. The absence of a clear chemical energy source for gliding motility and a positive correlation between speed and temperature suggest that energy derived from heat provides the major source of power for the gliding motor of M. penetrans.
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Abstract
The de novo synthesized polar lipids of Mycoplasma species are rather simple, comprising primarily of the acidic glycerophospholipids PG and CL. In addition, when grown in a medium containing serum, significant amounts of PC and SPM are incorporated into the mycoplasma cell membrane although these lipids are very uncommon in wall-covered bacteria. The exogenous lipids are either incorporated unchanged or the PC incorporated is modified by a deacylation-acylation enzymatic cycle to form disaturated PC. Although their small genome, in some Mycoplasma species, other genes involved in lipid biosynthesis were detected, resulting in the synthesis of a variety of glycolipis, phosphoglycolipids and ether lipids. We suggest that analyses and comparisons of mycoplasma polar lipids may serve as a novel and useful tool for classification. Nonetheless, to evaluate the importance of polar lipids in mycoplasma, further systematic and extensive studies on more Mycoplasma species are needed. While studies are needed to elucidate the role of lipids in the mechanisms governing the interaction of mycoplasmas with host eukaryotic cells, the finding that a terminal phosphocholine containing glycolipids of M. fermentans serves both as a major immune determinants and as a trigger of the inflammatory responses, and the findings that the fusogenicity of M. fermentans with host cells is markedly stimulated by lyso-ether lipids, are important steps toward understanding the molecular mechanisms of M. fermentans pathogenicity.
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Liu W, Fang L, Li M, Li S, Guo S, Luo R, Feng Z, Li B, Zhou Z, Shao G, Chen H, Xiao S. Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome. PLoS One 2012; 7:e35698. [PMID: 22536428 PMCID: PMC3335003 DOI: 10.1371/journal.pone.0035698] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 03/20/2012] [Indexed: 12/04/2022] Open
Abstract
Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain an improved understanding of essential genes. By analyzing the core genome of mycoplasmas, we finally revealed the conserved essential genes set for mycoplasma survival. Further analysis showed that the core genome set has many characteristics in common with experimentally identified essential genes. Several key genes, which are related to DNA replication and repair and can be disrupted in transposon mutagenesis studies, may be critical for bacteria survival especially over long period natural selection. Phylogenomic reconstructions based on 3,355 homologous groups allowed robust estimation of phylogenetic relatedness among mycoplasma strains. To obtain deeper insight into the relative roles of molecular evolution in pathogen adaptation to their hosts, we also analyzed the positive selection pressures on particular sites and lineages. There appears to be an approximate correlation between the divergence of species and the level of positive selection detected in corresponding lineages.
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Affiliation(s)
- Wei Liu
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Liurong Fang
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Mao Li
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Sha Li
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shaohua Guo
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Rui Luo
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhixin Feng
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Zhemin Zhou
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Guoqing Shao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China
| | - Huanchun Chen
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shaobo Xiao
- Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China
- * E-mail:
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Shu HW, Liu TT, Chan HI, Liu YM, Wu KM, Shu HY, Tsai SF, Hsiao KJ, Hu WS, Ng WV. Complexity of the Mycoplasma fermentans M64 genome and metabolic essentiality and diversity among mycoplasmas. PLoS One 2012; 7:e32940. [PMID: 22509252 PMCID: PMC3317919 DOI: 10.1371/journal.pone.0032940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 02/02/2012] [Indexed: 11/30/2022] Open
Abstract
Recently, the genomes of two Mycoplasma fermentans strains, namely M64 and JER, have been completely sequenced. Gross comparison indicated that the genome of M64 is significantly bigger than the other strain and the difference is mainly contributed by the repetitive sequences including seven families of simple and complex transposable elements ranging from 973 to 23,778 bps. Analysis of these repeats resulted in the identification of a new distinct family of Integrative Conjugal Elements of M. fermentans, designated as ICEF-III. Using the concept of “reaction connectivity”, the metabolic capabilities in M. fermentans manifested by the complete and partial connected biomodules were revealed. A comparison of the reported M. pulmonis, M. arthritidis, M. genitalium, B. subtilis, and E. coli essential genes and the genes predicted from the M64 genome indicated that more than 73% of the Mycoplasmas essential genes are preserved in M. fermentans. Further examination of the highly and partly connected reactions by a novel combinatorial phylogenetic tree, metabolic network, and essential gene analysis indicated that some of the pathways (e.g. purine and pyrimidine metabolisms) with partial connected reactions may be important for the conversions of intermediate metabolites. Taken together, in light of systems and network analyses, the diversity among the Mycoplasma species was manifested on the variations of their limited metabolic abilities during evolution.
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Affiliation(s)
- Hung-Wei Shu
- Laboratory Science in Medicine, Department of Biotechnology, Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Tze-Tze Liu
- Genome Research Center, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Huang-I Chan
- Institute of Biomedical Informatics, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Yen-Ming Liu
- Institute of Genome Sciences, Department of Life Sciences, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Keh-Ming Wu
- Genome Research Center, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Hung-Yu Shu
- Genome Research Center, National Yang Ming University, Taipei, Taiwan, Republic of China
| | - Shih-Feng Tsai
- Genome Research Center, National Yang Ming University, Taipei, Taiwan, Republic of China
- Institute of Genome Sciences, Department of Life Sciences, National Yang Ming University, Taipei, Taiwan, Republic of China
- Division of Molecular and Genome Medicine, National Health Research Institute, Zhunan Town, Miaoli County, Taiwan, Republic of China
| | - Kwang-Jen Hsiao
- Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan, Republic of China
- Department of Education and Research, Taipei City Hospital, Taipei, Taiwan, Republic of China
| | - Wensi S. Hu
- Laboratory Science in Medicine, Department of Biotechnology, Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
- * E-mail: (WSH); (WVN)
| | - Wailap Victor Ng
- Laboratory Science in Medicine, Department of Biotechnology, Institute of Biotechnology in Medicine, National Yang Ming University, Taipei, Taiwan, Republic of China
- Institute of Biomedical Informatics, National Yang Ming University, Taipei, Taiwan, Republic of China
- * E-mail: (WSH); (WVN)
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