1
|
Hammer TJ. Why do hosts malfunction without microbes? Missing benefits versus evolutionary addiction. Trends Microbiol 2024; 32:132-141. [PMID: 37652785 DOI: 10.1016/j.tim.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 09/02/2023]
Abstract
Microbes are widely recognized to be vital to host health. This new consensus rests, in part, on experiments showing how hosts malfunction when microbes are removed. More and more microbial dependencies are being discovered, even in fundamental processes such as development, immunity, physiology, and behavior. But why do they exist? The default explanation is that microbes are beneficial; when hosts lose microbes, they also lose benefits. Here I call attention to evolutionary addiction, whereby a host trait evolves a need for microbes without having been improved by them. Evolutionary addiction should be considered when interpreting microbe-removal experiments, as it is a distinct and potentially common process. Further, it may have unique implications for the evolution and stability of host-microbe interactions.
Collapse
Affiliation(s)
- Tobin J Hammer
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA.
| |
Collapse
|
2
|
Abstract
Symbiosis is a process that can generate evolutionary novelties and can extend the phenotypic niche space of organisms. Symbionts can act together with their hosts to co-construct host organs, within which symbionts are housed. Once established within hosts, symbionts can also influence various aspects of host phenotype, such as resource acquisition, protection from predation by acquisition of toxicity, as well as behaviour. Once symbiosis is established, its fidelity between generations must be ensured. Hosts evolve various mechanisms to screen unwanted symbionts and to facilitate faithful transmission of mutualistic partners between generations. Microbes are the most important symbionts that have influenced plant and animal phenotypes; multicellular organisms engage in developmental symbioses with microbes at many stages in ontogeny. The co-construction of niches may result in composite organisms that are physically nested within each other. While it has been advocated that these composite organisms need new evolutionary theories and perspectives to describe their properties and evolutionary trajectories, it appears that standard evolutionary theories are adequate to explore selection pressures on their composite or individual traits. Recent advances in our understanding of composite organisms open up many important questions regarding the stability and transmission of these units.
Collapse
Affiliation(s)
- Renee M Borges
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru 560 012, India.
| |
Collapse
|
3
|
Sullivan W. Wolbachia, bottled water, and the dark side of symbiosis. Mol Biol Cell 2017; 28:2343-2346. [PMID: 28855327 PMCID: PMC5576898 DOI: 10.1091/mbc.e17-02-0132] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/20/2017] [Accepted: 06/26/2017] [Indexed: 12/04/2022] Open
Abstract
Obligate endosymbiosis is operationally defined when loss or removal of the endosymbiont from the host results in the death of both. Whereas these relationships are typically viewed as mutualistic, molecular and cellular analysis reveals numerous instances in which these symbiotic relationships are established by alternative, nonmutualistic strategies. The endosymbiont usurps or integrates into core host processes, creating a need where none previously existed. Here I discuss examples of these addictive symbiotic relationships and how they are a likely outcome of all complex evolving systems.
Collapse
Affiliation(s)
- William Sullivan
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| |
Collapse
|
4
|
Abstract
Omics, including genomics, proteomics, and metabolomics, enable us to explain symbioses in terms of the underlying molecules and their interactions. The central task is to transform molecular catalogs of genes, metabolites, etc., into a dynamic understanding of symbiosis function. We review four exemplars of omics studies that achieve this goal, through defined biological questions relating to metabolic integration and regulation of animal-microbial symbioses, the genetic autonomy of bacterial symbionts, and symbiotic protection of animal hosts from pathogens. As omic datasets become increasingly complex, computationally sophisticated downstream analyses are essential to reveal interactions not evident from visual inspection of the data. We discuss two approaches, phylogenomics and transcriptional clustering, that can divide the primary output of omics studies-long lists of factors-into manageable subsets, and we describe how they have been applied to analyze large datasets and generate testable hypotheses.
Collapse
Affiliation(s)
- J Chaston
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York 14853, USA
| | | |
Collapse
|
5
|
Pajares MA, Markham GD. Methionine adenosyltransferase (s-adenosylmethionine synthetase). ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2011; 78:449-521. [PMID: 22220481 DOI: 10.1002/9781118105771.ch11] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- María A Pajares
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid Spain
| | | |
Collapse
|
6
|
Park M, Kim MS, Lee KM, Hwang SY, Ahn TI. Characterization of a cryptic plasmid from an alpha-proteobacterial endosymbiont of Amoeba proteus. Plasmid 2008; 61:78-87. [PMID: 18951917 DOI: 10.1016/j.plasmid.2008.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Revised: 09/21/2008] [Accepted: 09/23/2008] [Indexed: 10/21/2022]
Abstract
A new cryptic plasmid pAP3.9 was discovered in symbiotic alpha-proteobacteria present in the cytoplasm of Amoeba proteus. The plasmid is 3869bp with a GC content of 34.66% and contains replication origins for both double-strand (dso) and single-strand (sso). It has three putative ORFs encoding Mob, Rep and phosphoglycolate phosphatase (PGPase). The pAP3.9 plasmid appears to propagate by the conjugative rolling-circle replication (RCR), since it contains all required factors such as Rep, sso and dso. Mob and Rep showed highest similarities to those of the cryptic plasmid pBMYdx in Bacillus mycoides. The PGPase was homologous to that of Bacillus cereus and formed a clade with those of Bacillus sp. in molecular phylogeny. These results imply that the pAP3.9 plasmid evolved by the passage through Bacillus species. We hypothesize that the plasmid-encoded PGPase may have contributed to the establishment of bacterial symbiosis within the hostile environment of amoeba cytoplasm.
Collapse
Affiliation(s)
- Miey Park
- Department of Biological Science, Seoul National University, Kwanak-Gu, Seoul 151-742, Republic of Korea
| | | | | | | | | |
Collapse
|
7
|
Jeon TJ. DNA adenine methylation of sams1 gene in symbiont-bearing Amoeba proteus. J Microbiol 2008; 46:564-70. [DOI: 10.1007/s12275-008-0129-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Accepted: 08/18/2008] [Indexed: 12/13/2022]
|
8
|
Park M, Yun ST, Kim MS, Chun J, Ahn TI. Phylogenetic characterization of Legionella-like endosymbiotic X-bacteria in Amoeba proteus: a proposal for 'Candidatus Legionella jeonii' sp. nov. Environ Microbiol 2005; 6:1252-63. [PMID: 15560823 DOI: 10.1111/j.1462-2920.2004.00659.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The X-bacteria which initiated organismic association with the D strain of Amoeba proteus in 1966 as parasites have changed to obligate endosymbionts on which the host depends for survival. Owing to the difficulty in cultivating the bacteria in vitro, the identity of X-bacteria has not been determined. As the life cycle of X-bacteria is similar to that of Legionella spp. in soil amoebae, we applied the polymerase chain reaction method with specific primers aimed at Legionella spp. for the detection and cloning of 16S rRNA gene. The identity and intracellular localization of the endosymbiont were confirmed by the application of a specific fluorescently labelled 16S rRNA-targeted probe. In addition we cloned RNA polymerase beta-subunit gene (rpoB) of X-bacteria by genomic library tagging. A phylogenetic analysis of the 16S rRNA gene placed the bacterium within a unique monophyletic group containing all other members of the genus Legionella. Phylogeny from rpoB and mip genes further confirmed the taxonomic context of X-bacteria to be a Legionella sp. In all three phylogenic analyses, X-bacterium was placed apart from Legionella-like amoebal pathogens present in soil amoebae. Thus, we propose the name 'Candidatus Legionella jeonii' sp. nov. for the endosymbiotic X-bacteria in Amoeba proteus.
Collapse
MESH Headings
- Amino Acid Sequence
- Amoeba/microbiology
- Animals
- Bacterial Proteins/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- DNA-Directed RNA Polymerases/genetics
- Genes, rRNA
- Immunophilins/genetics
- In Situ Hybridization, Fluorescence
- Legionella/classification
- Legionella/genetics
- Legionella/isolation & purification
- Membrane Proteins/genetics
- Molecular Sequence Data
- Peptidylprolyl Isomerase/genetics
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Symbiosis
Collapse
Affiliation(s)
- Miey Park
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | | | | | | | | |
Collapse
|
9
|
Shivji M, Burger S, Moncada CA, Clarkson AB, Merali S. Effect of nicotine on lung S-adenosylmethionine and development of Pneumocystis pneumonia. J Biol Chem 2005; 280:15219-28. [PMID: 15668255 DOI: 10.1074/jbc.m413946200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Because S-adenosylmethionine (AdoMet) is required by Pneumocystis carinii in vitro, Pneumocystis infection depletes plasma AdoMet of rats and humans, nicotine reduces AdoMet of guinea pig lungs, and smoking correlates with reduced episodes of Pneumocystis pneumonia (PCP) in AIDS patients, we tested the effect of nicotine treatment on PCP using a rat model. Intraperitoneal infusion of 400 microg of R-(+) nicotine kg(-1) h(-1) intraperitoneal for 21 days caused a 15-fold reduction in lung AdoMet although neither plasma nor liver were changed. Infusion of 4 and 400 microg kg(-1) h(-1) into immunosuppressed rats, beginning when rats were inoculated with P. carinii, caused 85 and 99.88% reductions, respectively, in P. carinii cysts at sacrifice 21 days later; P. carinii nuclei were reduced by 91.2 and >99.99%, respectively. This effect was reversed by concomitant administration of AdoMet with nicotine. Treatment with AdoMet alone increased infection intensity. We conclude that AdoMet is a critical and limiting nutrient for Pneumocystis thus can serve as a therapeutic target for PCP. Regarding the mechanism, nicotine treatment caused no change in rat lung activity of AdoMet synthesizing methionine ATP transferase activity nor was there any evidence of increased AdoMet utilization for methylation reactions. Except of a doubling of putrescine, nicotine treatment also did not change lung polyamine content. However, key polyamine anabolic and catabolic enzymes were upregulated, and there were corresponding changes in polyamine metabolic intermediates. We conclude that chronic nicotine treatment increases lung polyamine catabolic/anabolic cycling and/or excretion leading to increased AdoMet-consuming polyamine biosynthesis and depletion of lung AdoMet.
Collapse
Affiliation(s)
- Mehboob Shivji
- Department of Medical and Molecular Parasitology, New York University School of Medicine, New York, New York 10010, USA
| | | | | | | | | |
Collapse
|
10
|
Abstract
Amoebae of the xD strain of Amoeba proteus that arose from the D strain by spontaneous infection of Legionella-like X-bacteria are now dependent on their symbionts for survival. Each xD amoeba contains about 42,000 symbionts within symbiosomes, and established xD amoebae die if their symbionts are removed. Thus, harmful infective bacteria changed into necessary cell components. As a result of harboring X-bacteria. xD amoebae exhibit various physiological and genetic characteristics that are different from those of symbiont-free D amoebae. One of the recent findings is that bacterial symbionts control the expression of a host's house-keeping gene. Thus, the expression of the normal amoeba sams gene (sams1) encoding one form of S-adenosylmethionine synthetase is switched to that of sams2 by endosymbiotic X-bacteria. Possible mechanisms for the switching of sams genes brought about by endosymbionts and its significance are discussed.
Collapse
Affiliation(s)
- Kwang W Jeon
- Department of Biochemistry, University of Tennessee, Knoxville, TN 37996, USA.
| |
Collapse
|
11
|
|
12
|
Abstract
The expression of genes for S-adenosylmethionine synthetase (SAMS), which catalyzes the synthesis of S-adenosylmethionine (AdoMet), a major methyl donor in cells, was studied in symbiont-free (D) and symbiont-bearing (xD) amoeba strains to determine the effect of bacterial endosymbionts. The symbionts suppressed the expression of the gene in host xD amoebae, but amoebae still exhibited about half the enzyme activity found in symbiont-free D amoebae. The study was aimed at elucidating mechanisms of the suppression of the amoeba's gene and determining the alternative source for the gene product. Unexpectedly, we found a second sams (sams2) gene in amoebae, which encoded 390 amino acids. Results of experiments measuring SAMS activities and amounts of AdoMet in D and xD amoebae showed that the half SAMS activity found in xD amoebae came from the amoeba's SAMS2 and not from their endosymbionts. The expression of amoeba sams genes was switched from sams1 to sams2 as a result of infection with X-bacteria, raising the possibility that the switch in the expression of sams genes by bacteria plays a role in the development of symbiosis and the host-pathogen interactions. This is the first report showing such a switch in the expression of host sams genes by infecting bacteria.
Collapse
Affiliation(s)
- Taeck J Jeon
- Department of Biochemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | |
Collapse
|