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All living cells are cognitive. Biochem Biophys Res Commun 2020; 564:134-149. [PMID: 32972747 DOI: 10.1016/j.bbrc.2020.08.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/28/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022]
Abstract
All living cells sense and respond to changes in external or internal conditions. Without that cognitive capacity, they could not obtain nutrition essential for growth, survive inevitable ecological changes, or correct accidents in the complex processes of reproduction. Wherever examined, even the smallest living cells (prokaryotes) display sophisticated regulatory networks establishing appropriate adaptations to stress conditions that maximize the probability of survival. Supposedly "simple" prokaryotic organisms also display remarkable capabilities for intercellular signalling and multicellular coordination. These observations indicate that all living cells are cognitive.
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Simultaneous Identification of Potential Pathogenicity Factors of Mycoplasma agalactiae in the Natural Ovine Host by Negative Selection. Infect Immun 2015; 83:2751-61. [PMID: 25916984 DOI: 10.1128/iai.00403-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/16/2015] [Indexed: 11/20/2022] Open
Abstract
Mycoplasmas possess complex pathogenicity determinants that are largely unknown at the molecular level. Mycoplasma agalactiae serves as a useful model to study the molecular basis of mycoplasma pathogenicity. The generation and in vivo screening of a transposon mutant library of M. agalactiae were employed to unravel its host colonization factors. Tn4001mod mutants were sequenced using a novel sequencing method, and functionally heterogeneous pools containing 15 to 19 selected mutants were screened simultaneously through two successive cycles of sheep intramammary infections. A PCR-based negative selection method was employed to identify mutants that failed to colonize the udders and draining lymph nodes in the animals. A total of 14 different mutants found to be absent from ≥ 95% of samples were identified and subsequently verified via a second round of stringent confirmatory screening where 100% absence was considered attenuation. Using this criterion, seven mutants with insertions in genes MAG1050, MAG2540, MAG3390, uhpT, eutD, adhT, and MAG4460 were not recovered from any of the infected animals. Among the attenuated mutants, many contain disruptions in hypothetical genes, implying their previously unknown role in M. agalactiae pathogenicity. These data indicate the putative role of functionally different genes, including hypothetical ones, in the pathogenesis of M. agalactiae. Defining the precise functions of the identified genes is anticipated to increase our understanding of M. agalactiae infections and to develop successful intervention strategies against it.
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Hegde S, Rosengarten R, Chopra-Dewasthaly R. Disruption of the pdhB pyruvate dehydrogenase [corrected] gene affects colony morphology, in vitro growth and cell invasiveness of Mycoplasma agalactiae. PLoS One 2015; 10:e0119706. [PMID: 25799063 PMCID: PMC4370745 DOI: 10.1371/journal.pone.0119706] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/14/2015] [Indexed: 12/16/2022] Open
Abstract
The utilization of available substrates, the metabolic potential and the growth rates of bacteria can play significant roles in their pathogenicity. This study concentrates on Mycoplasma agalactiae, which causes significant economic losses through its contribution to contagious agalactia in small ruminants by as yet unknown mechanisms. This lack of knowledge is primarily due to its fastidious growth requirements and the scarcity of genetic tools available for its manipulation and analysis. Transposon mutagenesis of M. agalactiae type strain PG2 resulted in several disruptions throughout the genome. A mutant defective in growth in vitro was found to have a transposon insertion in the pdhB gene, which encodes a component of the pyruvate dehydrogenase complex. This growth difference was quite significant during the actively dividing logarithmic phase but a gradual recovery was observed as the cells approached stationary phase. The mutant also exhibited a different and smaller colony morphology compared to the wild type strain PG2. For complementation, pdhAB was cloned downstream of a strong vpma promoter and upstream of a lacZ reporter gene in a newly constructed complementation vector. When transformed with this vector the pdhB mutant recovered its normal growth and colony morphology. Interestingly, the pdhB mutant also had significantly reduced invasiveness in HeLa cells, as revealed by double immunofluorescence staining. This deficiency was recovered in the complemented strain, which had invasiveness comparable to that of PG2. Taken together, these data indicate that pyruvate dehydrogenase might be an important player in infection with and colonization by M. agalactiae.
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Affiliation(s)
- Shivanand Hegde
- Division of Clinical Microbiology and Infection Biology, Institute of Bacteriology, Mycology and Hygiene, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Renate Rosengarten
- Division of Clinical Microbiology and Infection Biology, Institute of Bacteriology, Mycology and Hygiene, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Rohini Chopra-Dewasthaly
- Division of Clinical Microbiology and Infection Biology, Institute of Bacteriology, Mycology and Hygiene, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
- * E-mail:
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Bumgardner EA, Kittichotirat W, Bumgarner RE, Lawrence PK. Comparative genomic analysis of seven Mycoplasma hyosynoviae strains. Microbiologyopen 2015; 4:343-359. [PMID: 25693846 PMCID: PMC4398514 DOI: 10.1002/mbo3.242] [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: 10/27/2014] [Revised: 01/12/2015] [Accepted: 01/26/2015] [Indexed: 12/16/2022] Open
Abstract
Infection with Mycoplasma hyosynoviae can result in debilitating arthritis in pigs, particularly those aged 10 weeks or older. Strategies for controlling this pathogen are becoming increasingly important due to the rise in the number of cases of arthritis that have been attributed to infection in recent years. In order to begin to develop interventions to prevent arthritis caused by M. hyosynoviae, more information regarding the specific proteins and potential virulence factors that its genome encodes was needed. However, the genome of this emerging swine pathogen had not been sequenced previously. In this report, we present a comparative analysis of the genomes of seven strains of M. hyosynoviae isolated from different locations in North America during the years 2010 to 2013. We identified several putative virulence factors that may contribute to the ability of this pathogen to adhere to host cells. Additionally, we discovered several prophage genes present within the genomes of three strains that show significant similarity to MAV1, a phage isolated from the related species, M. arthritidis. We also identified CRISPR-Cas and type III restriction and modification systems present in two strains that may contribute to their ability to defend against phage infection.
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Affiliation(s)
| | - Weerayuth Kittichotirat
- Systems Biology and Bioinformatics Research Group, Pilot Plant, Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand
| | - Roger E Bumgarner
- Department of Microbiology, University of Washington, Seattle, Washington
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Algire MA, Montague MG, Vashee S, Lartigue C, Merryman C. A Type III restriction-modification system in Mycoplasma mycoides subsp. capri. Open Biol 2013; 2:120115. [PMID: 23155485 PMCID: PMC3498834 DOI: 10.1098/rsob.120115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 10/10/2012] [Indexed: 12/24/2022] Open
Abstract
The sequenced genome of Mycoplasma mycoides subsp. capri revealed the presence of a Type III restriction–modification system (MmyCI). The methyltransferase (modification) subunit of MmyCI (M.MmyCI) was shown to recognize the sequence 5′-TGAG-3′ and methylate the adenine. The coding region of the methyltransferase gene contains 12 consecutive AG dinucleotide repeats that result in a translational termination at a TAA codon immediately beyond the repeat region. This strain does not have MmyCI activity. A clone was found with 10 AG repeats such that the gene is in frame, and this strain has MmyCI activity, suggesting that the expression of the MmyCI methyltransferase may be phase variable.
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Affiliation(s)
- Mikkel A Algire
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
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Dybvig K, Lao P, Jordan DS, Simmons WL. Fewer essential genes in mycoplasmas than previous studies suggest. FEMS Microbiol Lett 2010; 311:51-5. [PMID: 20722737 DOI: 10.1111/j.1574-6968.2010.02078.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Here, we describe mutants of Mycoplasma pulmonis that were obtained using a minitransposon, Tn4001TF1, which actively transposes but is then unable to undergo subsequent excision events. Using Tn4001TF1, we disrupted 39 genes previously thought to be essential for growth. Thus, the number of genes required for growth has been overestimated. This study also revealed evidence of gene duplications in M. pulmonis and identified chromosome segregation proteins that are dispensable in mycoplasmas but essential in Bacillus subtilis.
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Affiliation(s)
- Kevin Dybvig
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
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Pereyre S, Sirand-Pugnet P, Beven L, Charron A, Renaudin H, Barré A, Avenaud P, Jacob D, Couloux A, Barbe V, de Daruvar A, Blanchard A, Bébéar C. Life on arginine for Mycoplasma hominis: clues from its minimal genome and comparison with other human urogenital mycoplasmas. PLoS Genet 2009; 5:e1000677. [PMID: 19816563 PMCID: PMC2751442 DOI: 10.1371/journal.pgen.1000677] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 09/07/2009] [Indexed: 12/24/2022] Open
Abstract
Mycoplasma hominis is an opportunistic human mycoplasma. Two other pathogenic human species, M. genitalium and Ureaplasma parvum, reside within the same natural niche as M. hominis: the urogenital tract. These three species have overlapping, but distinct, pathogenic roles. They have minimal genomes and, thus, reduced metabolic capabilities characterized by distinct energy-generating pathways. Analysis of the M. hominis PG21 genome sequence revealed that it is the second smallest genome among self-replicating free living organisms (665,445 bp, 537 coding sequences (CDSs)). Five clusters of genes were predicted to have undergone horizontal gene transfer (HGT) between M. hominis and the phylogenetically distant U. parvum species. We reconstructed M. hominis metabolic pathways from the predicted genes, with particular emphasis on energy-generating pathways. The Embden–Meyerhoff–Parnas pathway was incomplete, with a single enzyme absent. We identified the three proteins constituting the arginine dihydrolase pathway. This pathway was found essential to promote growth in vivo. The predicted presence of dimethylarginine dimethylaminohydrolase suggested that arginine catabolism is more complex than initially described. This enzyme may have been acquired by HGT from non-mollicute bacteria. Comparison of the three minimal mollicute genomes showed that 247 CDSs were common to all three genomes, whereas 220 CDSs were specific to M. hominis, 172 CDSs were specific to M. genitalium, and 280 CDSs were specific to U. parvum. Within these species-specific genes, two major sets of genes could be identified: one including genes involved in various energy-generating pathways, depending on the energy source used (glucose, urea, or arginine) and another involved in cytadherence and virulence. Therefore, a minimal mycoplasma cell, not including cytadherence and virulence-related genes, could be envisaged containing a core genome (247 genes), plus a set of genes required for providing energy. For M. hominis, this set would include 247+9 genes, resulting in a theoretical minimal genome of 256 genes. Mycoplasma hominis, M. genitalium, and Ureaplasma parvum are human pathogenic bacteria that colonize the urogenital tract. They have minimal genomes, and thus have a minimal metabolic capacity. However, they have distinct energy-generating pathways and distinct pathogenic roles. We compared the genomes of these three human pathogen minimal species, providing further insight into the composition of hypothetical minimal gene sets needed for life. To this end, we sequenced the whole M. hominis genome and reconstructed its energy-generating pathways from gene predictions. Its unusual major energy-producing pathway through arginine hydrolysis was confirmed in both genome analyses and in vivo assays. Our findings suggest that M. hominis and U. parvum underwent genetic exchange, probably while sharing a common host. We proposed a set of genes likely to represent a minimal genome. For M. hominis, this minimal genome, not including cytadherence and virulence-related genes, can be defined comprising the 247 genes shared by the three minimal genital mollicutes, combined with a set of nine genes needed for energy production for cell metabolism. This study provides insight for the synthesis of artificial genomes.
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Affiliation(s)
- Sabine Pereyre
- Université de Bordeaux, Laboratoire de Bactériologie EA 3671, Bordeaux, France
| | - Pascal Sirand-Pugnet
- INRA, UMR 1090, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1090, Villenave d'Ornon, France
| | - Laure Beven
- INRA, UMR 1090, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1090, Villenave d'Ornon, France
| | - Alain Charron
- Université de Bordeaux, Laboratoire de Bactériologie EA 3671, Bordeaux, France
| | - Hélène Renaudin
- Université de Bordeaux, Laboratoire de Bactériologie EA 3671, Bordeaux, France
| | - Aurélien Barré
- Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Bordeaux, France
| | - Philippe Avenaud
- Université de Bordeaux, Laboratoire de Bactériologie EA 3671, Bordeaux, France
| | - Daniel Jacob
- Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Bordeaux, France
| | | | - Valérie Barbe
- Génoscope, Centre National de Séquençage, Evry, France
| | - Antoine de Daruvar
- Université de Bordeaux, Centre de Bioinformatique de Bordeaux, Bordeaux, France
- CNRS UMR 5800, Laboratoire Bordelais de Recherche en Informatique, Talence, France
| | - Alain Blanchard
- INRA, UMR 1090, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1090, Villenave d'Ornon, France
| | - Cécile Bébéar
- Université de Bordeaux, Laboratoire de Bactériologie EA 3671, Bordeaux, France
- * E-mail:
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Adamczyk-Poplawska M, Lower M, Piekarowicz A. Characterization of the NgoAXP: phase-variable type III restriction-modification system in Neisseria gonorrhoeae. FEMS Microbiol Lett 2009; 300:25-35. [PMID: 19758331 DOI: 10.1111/j.1574-6968.2009.01760.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Methyltransferases associated with type III restriction-modification (RM) systems are phase-variably expressed in a variety of pathogenic bacteria. NgoAXP, the type III RM system encoded by Neisseria gonorrhoeae, was characterized in this study. The cloned resngoAXP and ngoAXPmod genes were expressed in Escherichia coli strains. The restriction and modification activities of NgoAXP were confirmed in vivo by the lambda phage restriction and modification test and in vitro by the methylation of DNA substrates in the presence of [methyl-(3)H]AdoMet. As in all known type III systems, the restriction activity needed the presence of both genes, while the presence of the ngoAXPmod gene was sufficient for DNA methylation. Following its overexpression, the DNA methyltransferase M.NgoAXP was purified to apparent homogeneity using metal affinity chromatography. The specific sequence recognized by this enzyme was determined as a nonpalindromic sequence: 5'-CCACC-3', in which the adenine residue is methylated. We observed that in E. coli cells, the expression of the restriction phenotype associated with NgoAXP switched randomly. This phase variation was associated with the change in the number of pentanucleotide repeats (5'-CCAAC/G-3') present at the 5'-end of the coding region of the ngoAXPmod gene.
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Cocquyt E, Verbruggen H, Leliaert F, Zechman FW, Sabbe K, De Clerck O. Gain and loss of elongation factor genes in green algae. BMC Evol Biol 2009; 9:39. [PMID: 19216746 PMCID: PMC2652445 DOI: 10.1186/1471-2148-9-39] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 02/12/2009] [Indexed: 11/15/2022] Open
Abstract
Background Two key genes of the translational apparatus, elongation factor-1 alpha (EF-1α) and elongation factor-like (EFL) have an almost mutually exclusive distribution in eukaryotes. In the green plant lineage, the Chlorophyta encode EFL except Acetabularia where EF-1α is found, and the Streptophyta possess EF-1α except Mesostigma, which has EFL. These results raise questions about evolutionary patterns of gain and loss of EF-1α and EFL. A previous study launched the hypothesis that EF-1α was the primitive state and that EFL was gained once in the ancestor of the green plants, followed by differential loss of EF-1α or EFL in the principal clades of the Viridiplantae. In order to gain more insight in the distribution of EF-1α and EFL in green plants and test this hypothesis we screened the presence of the genes in a large sample of green algae and analyzed their gain-loss dynamics in a maximum likelihood framework using continuous-time Markov models. Results Within the Chlorophyta, EF-1α is shown to be present in three ulvophycean orders (i.e., Dasycladales, Bryopsidales, Siphonocladales) and the genus Ignatius. Models describing gene gain-loss dynamics revealed that the presence of EF-1α, EFL or both genes along the backbone of the green plant phylogeny is highly uncertain due to sensitivity to branch lengths and lack of prior knowledge about ancestral states or rates of gene gain and loss. Model refinements based on insights gained from the EF-1α phylogeny reduce uncertainty but still imply several equally likely possibilities: a primitive EF-1α state with multiple independent EFL gains or coexistence of both genes in the ancestor of the Viridiplantae or Chlorophyta followed by differential loss of one or the other gene in the various lineages. Conclusion EF-1α is much more common among green algae than previously thought. The mutually exclusive distribution of EF-1α and EFL is confirmed in a large sample of green plants. Hypotheses about the gain-loss dynamics of elongation factor genes are hard to test analytically due to a relatively flat likelihood surface, even if prior knowledge is incorporated. Phylogenetic analysis of EFL genes indicates misinterpretations in the recent literature due to uncertainty regarding the root position.
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Affiliation(s)
- Ellen Cocquyt
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium.
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French CT, Lao P, Loraine AE, Matthews BT, Yu H, Dybvig K. Large-scale transposon mutagenesis of Mycoplasma pulmonis. Mol Microbiol 2008; 69:67-76. [PMID: 18452587 DOI: 10.1111/j.1365-2958.2008.06262.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To obtain mutants for the study of the basic biology and pathogenic mechanisms of mycoplasmas, the insertion site of transposon Tn4001T was determined for 1700 members of a library of Mycoplasma pulmonis mutants. After evaluating several criteria for gene disruption, we concluded that 321 of the 782 protein coding regions were inactivated. The dispensable and essential genes of M. pulmonis were compared with those reported for Mycoplasma genitalium and Bacillus subtilis. Perhaps the most surprising result of the current study was that unlike other bacteria, ribosomal proteins S18 and L28 were dispensable. Carbohydrate transport and the susceptibility of selected mutants to UV irradiation were examined to assess whether active transposition of Tn4001T within the genome would confound phenotypic analysis. In contrast to earlier reports suggesting that mycoplasmas were limited in their DNA repair machinery, mutations in recA, uvrA, uvrB and uvrC resulted in a DNA-repair deficient phenotype. A mutant with a defect in transport of N-acetylglucosamine was identified.
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Affiliation(s)
- Christopher T French
- Department of Genetics, University of Alabama Birmingham, Birmingham, AL 35294, USA
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