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From Pathogens to Cancer: Are Cancer Cells Evolved Mitochondrial Super Cells? Diagnostics (Basel) 2023; 13:diagnostics13040813. [PMID: 36832301 PMCID: PMC9954806 DOI: 10.3390/diagnostics13040813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/07/2023] [Accepted: 02/19/2023] [Indexed: 02/23/2023] Open
Abstract
Life is based on a highly specific combination of atoms, metabolism, and genetics which eventually reflects the chemistry of the Universe which is composed of hydrogen, oxygen, nitrogen, sulfur, phosphorus, and carbon. The interaction of atomic, metabolic, and genetic cycles results in the organization and de-organization of chemical information of that which we consider as living entities, including cancer cells. In order to approach the problem of the origin of cancer it is therefore reasonable to start from the assumption that the sub-molecular level, the atomic structure, should be the considered starting point on which metabolism, genetics, and external insults eventually emanate. Second, it is crucial to characterize which of the entities and parts composing human cells may live a separate life; certainly, this theoretical standpoint would consider mitochondria, an organelle of "bacteria" origin embedded in conditions favorable for the onset of both. This organelle has not only been tolerated by immunity but has also been placed as a central regulator of cell defense. Virus, bacteria, and mitochondria are also similar in the light of genetic and metabolic elements; they share not only equivalent DNA and RNA features but also many basic biological activities. Thus, it is important to finalize that once the cellular integrity has been constantly broken down, the mitochondria like any other virus or bacteria return to their original autonomy to simply survive. The Warburg's law that states the ability of cancers to ferment glucose in the presence of oxygen, indicates mitochondria respiration abnormalities may be the underlying cause of this transformation towards super cancer cells. Though genetic events play a key part in altering biochemical metabolism, inducing aerobic glycolysis, this is not enough to impair mitochondrial function since mitochondrial biogenesis and quality control are constantly upregulated in cancers. While some cancers have mutations in the nuclear-encoded mitochondrial tricarboxylic acid (TCA) cycle, enzymes that produce oncogenic metabolites, there is also a bio-physic pathway for pathogenic mitochondrial genome mutations. The atomic level of all biological activities can be considered the very beginning, marked by the electron abnormal behavior that consequently affects DNA of both cells and mitochondria. Whilst the cell's nucleus DNA after a certain number of errors and defection tends to gradually switch off, the mitochondria DNA starts adopting several escape strategies, switching-on a few important genes that belong back at their original roots as independent beings. The ability to adopt this survival trick, by becoming completely immune to current life-threatening events, is probably the beginning of a differentiation process towards a "super-power cell", the cancer cells that remind many pathogens, including virus, bacteria, and fungi. Thus, here, we present a hypothesis regarding those changes that first begin at the mitochondria atomic level to steadily involve molecular, tissue and organ levels in response to the virus or bacteria constant insults that drive a mitochondria itself to become an "immortal cancer cell". Improved insights into this interplay between these pathogens and mitochondria progression may disclose newly epistemological paradigms as well as innovative procedures in targeting cancer cell progressive invasion.
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McLaughlin RW. Robinsoniella peoriensis: an emerging pathogen with few virulence factors. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2023; 26:135-142. [PMID: 36219351 DOI: 10.1007/s10123-022-00281-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 01/06/2023]
Abstract
Robinsoniella peoriensis is a Gram-positive bacterium which is anaerobic, spore-forming, and non-motile. It was initially isolated and characterized from feces and swine manure. Strains of this species have since been identified from different mammalian and non-mammalian gastrointestinal tracts. Strains have also been isolated from a variety of human infections, such as bacteremia, bone infections, and skin structures. R. peoriensis has recently been reported as causative for pyometra, which could result in death in the absence of sufficient antimicrobial treatment. However, to the author's knowledge, there has not been a single virulence factor identified. A major challenge of modern medicine is the failure of conventional procedures to characterize the capability of an emerging pathogen to cause disease. The goal of this study is to initially characterize the pathogenicity of this bacterium using a pathogenomics approach.
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Bhattacharya D, Etten JV, Benites LF, Stephens TG. Endosymbiotic ratchet accelerates divergence after organelle origin: The Paulinella model for plastid evolution: The Paulinella model for plastid evolution. Bioessays 2023; 45:e2200165. [PMID: 36328783 DOI: 10.1002/bies.202200165] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
We hypothesize that as one of the most consequential events in evolution, primary endosymbiosis accelerates lineage divergence, a process we refer to as the endosymbiotic ratchet. Our proposal is supported by recent work on the photosynthetic amoeba, Paulinella, that underwent primary plastid endosymbiosis about 124 Mya. This amoeba model allows us to explore the early impacts of photosynthetic organelle (plastid) origin on the host lineage. The current data point to a central role for effective population size (Ne ) in accelerating divergence post-endosymbiosis due to limits to dispersal and reproductive isolation that reduce Ne , leading to local adaptation. We posit that isolated populations exploit different strategies and behaviors and assort themselves in non-overlapping niches to minimize competition during the early, rapid evolutionary phase of organelle integration. The endosymbiotic ratchet provides a general framework for interpreting post-endosymbiosis lineage evolution that is driven by disruptive selection and demographic and population shifts. Also see the video abstract here: https://youtu.be/gYXrFM6Zz6Q.
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Affiliation(s)
- Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
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Abstract
The social amoeba Dictyostelium discoideum is a predatory soil protist frequently used for studying host-pathogen interactions. A subset of D. discoideum strains isolated from soil persistently carry symbiotic Paraburkholderia, recently formally described as P. agricolaris, P. bonniea, and P. hayleyella. The three facultative symbiont species of D. discoideum present a unique opportunity to study a naturally occurring symbiosis in a laboratory model protist. There is a large difference in genome size between P. agricolaris (8.7 million base pairs [Mbp]) versus P. hayleyella and P. bonniea (4.1 Mbp). We took a comparative genomics approach and compared the three genomes of D. discoideum symbionts to 12 additional Paraburkholderia genomes to test for genome evolution patterns that frequently accompany host adaptation. Overall, P. agricolaris is difficult to distinguish from other Paraburkholderia based on its genome size and content, but the reduced genomes of P. bonniea and P. hayleyella display characteristics indicative of genome streamlining rather than deterioration during adaptation to their protist hosts. In addition, D. discoideum-symbiont genomes have increased secretion system and motility genes that may mediate interactions with their host. Specifically, adjacent BurBor-like type 3 and T6SS-5-like type 6 secretion system operons shared among all three D. discoideum-symbiont genomes may be important for host interaction. Horizontal transfer of these secretion system operons within the amoeba host environment may have contributed to the unique ability of these symbionts to establish and maintain a symbiotic relationship with D. discoideum. IMPORTANCE Protists are a diverse group of typically single cell eukaryotes. Bacteria and archaea that form long-term symbiotic relationships with protists may evolve in additional ways than those in relationships with multicellular eukaryotes such as plants, animals, or fungi. Social amoebas are a predatory soil protist sometimes found with symbiotic bacteria living inside their cells. They present a unique opportunity to explore a naturally occurring symbiosis in a protist frequently used for studying host-pathogen interactions. We show that one amoeba-symbiont species is similar to other related bacteria in genome size and content, while the two reduced-genome-symbiont species show characteristics of genome streamlining rather than deterioration during adaptation to their host. We also identify sets of genes present in all three amoeba-symbiont genomes that are potentially used for host-symbiont interactions. Because the amoeba symbionts are distantly related, the amoeba host environment may be where these genes were shared among symbionts.
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Guo LT, Amikura K, Jiang HK, Mukai T, Fu X, Wang YS, O'Donoghue P, Söll D, Tharp JM. Ancestral Archaea Expanded the Genetic Code with Pyrrolysine. J Biol Chem 2022; 298:102521. [PMID: 36152750 DOI: 10.1016/j.jbc.2022.102521] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022] Open
Abstract
The pyrrolysyl-tRNA synthetase (PylRS) facilitates the co-translational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain highly active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Ca. Methanomethylophilus alvus. We show that, compared to the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency, but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 tRNAPyl sequences from diverse anaerobic archaea and bacteria. This analysis suggests that the PylRS•tRNAPyl pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the co-evolutionary history of PylRS and tRNAPyl and reveal the emergence of tRNAPyl sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNAPyl species with the more common G73-containing tRNAPyl will enable future efforts to engineer PylRS systems for further genetic code expansion.
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Affiliation(s)
- Li-Tao Guo
- Department of Molecular Biophysics & Biochemistry
| | - Kazuaki Amikura
- Department of Molecular Biophysics & Biochemistry; Department of Interdisciplinary Space Science, Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Kanagawa, Japan
| | - Han-Kai Jiang
- Institute of Biological Chemistry; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Takahito Mukai
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Xian Fu
- BGI-Shenzhen, Shenzhen, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Yane-Shih Wang
- Institute of Biological Chemistry; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Canada; Department of Chemistry, The University of Western Ontario, London, Canada
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry; Department of Chemistry, Yale University, New Haven, CT, USA
| | - Jeffery M Tharp
- Department of Molecular Biophysics & Biochemistry; Department of Chemistry, The University of Western Ontario, London, Canada.
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Amandine C, Ebert D, Stukenbrock E, Rodríguez de la Vega RC, Tiffin P, Croll D, Tellier A. Unraveling coevolutionary dynamics using ecological genomics. Trends Genet 2022; 38:1003-1012. [PMID: 35715278 DOI: 10.1016/j.tig.2022.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Coevolutionary interactions, from the delicate co-dependency in mutualistic interactions to the antagonistic relationship of hosts and parasites, are a ubiquitous driver of adaptation. Surprisingly, little is known about the genomic processes underlying coevolution in an ecological context. However, species comprise genetically differentiated populations that interact with temporally variable abiotic and biotic environments. We discuss the recent advances in coevolutionary theory and genomics as well as shortcomings, to identify coevolving genes that take into account this spatial and temporal variability of coevolution, and propose a practical guide to understand the dynamic of coevolution using an ecological genomics lens.
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Affiliation(s)
- Cornille Amandine
- Université Paris Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France.
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Eva Stukenbrock
- Max Planck Institute for Terrestrial Microbiology, Max Planck Research Group, Fungal Biodiversity, Marburg, Germany
| | | | - Peter Tiffin
- Department of Plant and Microbial Biology, 250 Biological Sciences, 1445 Gortner Ave., University of Minnesota, Saint Paul, MN 55108, USA
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland.
| | - Aurélien Tellier
- Population Genetics, Department of Life Science Systems, Technical University of Munich, Liesel-Beckman-Str. 2, 85354 Freising, Germany.
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Tougeron K, Iltis C. Impact of heat stress on the fitness outcomes of symbiotic infection in aphids: a meta-analysis. Proc Biol Sci 2022; 289:20212660. [PMID: 35350854 PMCID: PMC8965392 DOI: 10.1098/rspb.2021.2660] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Beneficial microorganisms shape the evolutionary trajectories of their hosts, facilitating or constraining the colonization of new ecological niches. One convincing example entails the responses of insect-microbe associations to rising temperatures. Indeed, insect resilience to stressful high temperatures depends on the genetic identity of the obligate symbiont and the presence of heat-protective facultative symbionts. As extensively studied organisms, aphids and their endosymbiotic bacteria represent valuable models to address eco-evolutionary questions about the thermal ecology of insect-microbe partnerships, with broad relevance to various biological systems and insect models. This meta-analysis aims to quantify the context-dependent impacts of symbionts on host phenotype in benign or stressful heat conditions, across fitness traits, types of heat stress and symbiont species. We found that warming lowered the benefits (resistance to parasitoids) and costs (development, fecundity) of infection by facultative symbionts, which was overall mostly beneficial to the hosts under short-term heat stress (heat shock) rather than extended warming. Heat-tolerant genotypes of the obligate symbiont Buchnera aphidicola and some facultative symbionts (Rickettsia sp., Serratia symbiotica) improved or maintained aphid fitness under heat stress. We discuss the implications of these findings for the general understanding of the cost-benefit balance of insect-microbe associations across multiple traits and their eco-evolutionary dynamics faced with climate change.
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Affiliation(s)
- Kévin Tougeron
- Earth and Life Institute, Ecology and Biodiversity, Université catholique de Louvain, Louvain-la-Neuve, Belgium,UMR CNRS 7058-EDYSAN, Université de Picardie Jules Verne, Amiens, France
| | - Corentin Iltis
- Earth and Life Institute, Ecology and Biodiversity, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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Pons I, Scieur N, Dhondt L, Renard ME, Renoz F, Hance T. Pervasiveness of the symbiont Serratia symbiotica in the aphid natural environment: distribution, diversity and evolution at a multitrophic level. FEMS Microbiol Ecol 2022; 98:6526308. [PMID: 35142841 DOI: 10.1093/femsec/fiac012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/05/2022] [Accepted: 02/08/2022] [Indexed: 11/12/2022] Open
Abstract
Symbioses are significant drivers of insect evolutionary ecology. Despite recent findings that these associations can emerge from environmentally derived bacterial precursors, there is still little information on how these potential progenitors of insect symbionts circulate in trophic systems. Serratia symbiotica represents a valuable model for deciphering evolutionary scenarios of bacterial acquisition by insects, as its diversity includes gut-associated strains that retained the ability to live independently of their hosts, representing a potential reservoir for symbioses emergence. Here, we conducted a field study to examine the distribution and diversity of S. symbiotica found in aphid populations, and in different compartments of their surrounding environment. Twenty % of aphids colonies were infected with S. symbiotica, including a wide diversity of strains with varied tissue tropism corresponding to different lifestyle. We also showed that the prevalence of S. symbiotica is influenced by seasonal temperatures. We found that S. symbiotica was present in non-aphid species and in host plants, and that its prevalence in these samples was higher when associated aphid colonies were infected. Furthermore, phylogenetic analyses suggest the existence of horizontal transfers between the different trophic levels. These results provide a new picture of the pervasiveness of an insect symbiont in nature.
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Affiliation(s)
- Inès Pons
- Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Nora Scieur
- Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Linda Dhondt
- Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Marie-Eve Renard
- Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - François Renoz
- Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
| | - Thierry Hance
- Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
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Uthanumallian K, Iha C, Repetti SI, Chan CX, Bhattacharya D, Duchene S, Verbruggen H. Tightly Constrained Genome Reduction and Relaxation of Purifying Selection during Secondary Plastid Endosymbiosis. Mol Biol Evol 2022; 39:msab295. [PMID: 34613411 PMCID: PMC8763093 DOI: 10.1093/molbev/msab295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Endosymbiosis, the establishment of a former free-living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids or chloroplasts, the light-harvesting organelle of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin has occurred multiple times in evolution. Here, we investigate the genomic signature of molecular processes acting through secondary plastid endosymbiosis-the origination of a new plastid from a free-living eukaryotic alga. We used phylogenetic comparative methods to study gene loss and changes in selective regimes on plastid genomes, focusing on green algae that have given rise to three independent lineages with secondary plastids (euglenophytes, chlorarachniophytes, and Lepidodinium). Our results show an overall increase in gene loss associated with secondary endosymbiosis, but this loss is tightly constrained by the retention of genes essential for plastid function. The data show that secondary plastids have experienced temporary relaxation of purifying selection during secondary endosymbiosis. However, this process is tightly constrained, with selection relaxed only relative to the background in primary plastids. Purifying selection remains strong in absolute terms even during the endosymbiosis events. Selection intensity rebounds to pre-endosymbiosis levels following endosymbiosis events, demonstrating the changes in selection efficiency during different origin phases of secondary plastids. Independent endosymbiosis events in the euglenophytes, chlorarachniophytes, and Lepidodinium differ in their degree of relaxation of selection, highlighting the different evolutionary contexts of these events. This study reveals the selection-drift interplay during secondary endosymbiosis and evolutionary parallels during organellogenesis.
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Affiliation(s)
| | - Cintia Iha
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Sebastian Duchene
- Deptartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
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Stever H, Eiben J, Bennett GM. Hawaiian Nysius Insects Rely on an Obligate Symbiont with a Reduced Genome That Retains a Discrete Nutritional Profile to Match Their Plant Seed Diet. Genome Biol Evol 2021; 13:6349176. [PMID: 34383896 PMCID: PMC8412300 DOI: 10.1093/gbe/evab189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 12/19/2022] Open
Abstract
Seed-feeding Nysius insects (Hemiptera: Lygaeidae) have a symbiotic association with distinct intracellular bacteria, “Candidatus Schneideria nysicola” (Gammaproteobacteria). Although many other hemipteran insect groups generally rely on bacterial symbionts that synthesize all ten essential amino acids lacking in their plant sap diets, the nutritional role of Schneideria in Nysius hosts that specialize on a more nutritionally complete seed-based diet has remained unknown. To determine the nutritional and functional capabilities of Schneideria, we sequenced the complete Schneideria genomes from three distantly related endemic Hawaiian Nysius seed bug species. The complete Schneideria genomes are highly conserved and perfectly syntenic among Hawaiian Nysius host species. Each circular chromosome is ∼0.57 Mb in size and encodes 537 protein-coding genes. They further exhibit a strong A + T nucleotide substitution bias with an average G + C nucleotide content of 29%. The predicted nutritional contribution of Schneideria includes four B vitamins and five of the ten essential amino acids that likely match its hosts’ seed-based diet. Disrupted and degraded genes in Schneideria suggests that Hawaiian lineages are undergoing continued gene losses observed in the smaller genomes of the other more ancient hemipteran symbionts.
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Affiliation(s)
- Heather Stever
- Department of Life and Environmental Sciences, University of California, Merced, USA
| | - Jesse Eiben
- Department of Biology, Geology, and Environmental Sciences, California University of Pennsylvania, USA
| | - Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, USA
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11
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Abstract
Spiders (Araneae) make up a remarkably diverse lineage of predators that have successfully colonized most terrestrial ecosystems. All spiders produce silk, and many species use it to build capture webs with an extraordinary diversity of forms. Spider diversity is distributed in a highly uneven fashion across lineages. This strong imbalance in species richness has led to several causal hypotheses, such as codiversification with insects, key innovations in silk structure and web architecture, and loss of foraging webs. Recent advances in spider phylogenetics have allowed testing of some of these hypotheses, but results are often contradictory, highlighting the need to consider additional drivers of spider diversification. The spatial and historical patterns of diversity and diversification remain contentious. Comparative analyses of spider diversification will advance only if we continue to make progress with studies of species diversity, distribution, and phenotypic traits, together with finer-scale phylogenies and genomic data.
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Affiliation(s)
- Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, 5020 Bergen, Norway;
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA;
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12
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Spencer HG. Beyond Equilibria: The Neglected Role of History in Ecology and Evolution. THE QUARTERLY REVIEW OF BIOLOGY 2020. [DOI: 10.1086/711803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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13
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Bourguignon T, Kinjo Y, Villa-Martín P, Coleman NV, Tang Q, Arab DA, Wang Z, Tokuda G, Hongoh Y, Ohkuma M, Ho SY, Pigolotti S, Lo N. Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes. Curr Biol 2020; 30:3848-3855.e4. [DOI: 10.1016/j.cub.2020.07.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/27/2020] [Accepted: 07/09/2020] [Indexed: 01/08/2023]
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14
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Salcedo-Porras N, Umaña-Diaz C, de Oliveira Barbosa Bitencourt R, Lowenberger C. The Role of Bacterial Symbionts in Triatomines: An Evolutionary Perspective. Microorganisms 2020; 8:E1438. [PMID: 32961808 PMCID: PMC7565714 DOI: 10.3390/microorganisms8091438] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/10/2020] [Accepted: 09/17/2020] [Indexed: 12/16/2022] Open
Abstract
Insects have established mutualistic symbiotic interactions with microorganisms that are beneficial to both host and symbiont. Many insects have exploited these symbioses to diversify and expand their ecological ranges. In the Hemiptera (i.e., aphids, cicadas, and true bugs), symbioses have established and evolved with obligatory essential microorganisms (primary symbionts) and with facultative beneficial symbionts (secondary symbionts). Primary symbionts are usually intracellular microorganisms found in insects with specialized diets such as obligate hematophagy or phytophagy. Most Heteroptera (true bugs), however, have gastrointestinal (GI) tract extracellular symbionts with functions analogous to primary endosymbionts. The triatomines, are vectors of the human parasite, Trypanosoma cruzi. A description of their small GI tract microbiota richness was based on a few culturable microorganisms first described almost a century ago. A growing literature describes more complex interactions between triatomines and bacteria with properties characteristic of both primary and secondary symbionts. In this review, we provide an evolutionary perspective of beneficial symbioses in the Hemiptera, illustrating the context that may drive the evolution of symbioses in triatomines. We highlight the diversity of the triatomine microbiota, bacterial taxa with potential to be beneficial symbionts, the unique characteristics of triatomine-bacteria symbioses, and the interactions among trypanosomes, microbiota, and triatomines.
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Affiliation(s)
- Nicolas Salcedo-Porras
- Centre for Cell Biology, Development and Disease, Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (C.U.-D.); (R.d.O.B.B.); (C.L.)
| | - Claudia Umaña-Diaz
- Centre for Cell Biology, Development and Disease, Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (C.U.-D.); (R.d.O.B.B.); (C.L.)
| | - Ricardo de Oliveira Barbosa Bitencourt
- Centre for Cell Biology, Development and Disease, Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (C.U.-D.); (R.d.O.B.B.); (C.L.)
- Programa de Pós-graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro, 23890-000 Seropédica, Brasil
| | - Carl Lowenberger
- Centre for Cell Biology, Development and Disease, Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; (C.U.-D.); (R.d.O.B.B.); (C.L.)
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Bohlin J, Rose B, Brynildsrud O, Birgitte Freiesleben De Blasio. A simple stochastic model describing genomic evolution over time of GC content in microbial symbionts. J Theor Biol 2020; 503:110389. [PMID: 32634385 DOI: 10.1016/j.jtbi.2020.110389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/21/2020] [Accepted: 06/24/2020] [Indexed: 11/29/2022]
Abstract
An organism's genomic base composition is usually summarized by its AT or GC content due to Chargaff's parity laws. Variation in prokaryotic GC content can be substantial between taxa but is generally small within microbial genomes. This variation has been found to correlate with both phylogeny and environmental factors. Since novel single-nucleotide polymorphisms (SNPs) within genomes are at least partially linked to the environment through natural selection, SNP GC content can be considered a compound measure of an organism's environmental influences, lifestyle, phylogeny as well as other more or less random processes. While there are several models describing genomic GC content few, if any, consider AT/GC mutation rates subjected to random perturbations. We present a mathematical model that describes how GC content in microbial genomes evolves over time as a function of the AT → GC and GC → AT mutation rates with Gaussian white noise disturbances. The model, which is suited specifically to non-recombining vertically transmitted prokaryotic symbionts, suggests that small differences in the AT/GC mutation rates can lead to profound differences in outcome due to the ensuing stochastic process. In other words, the model indicates that time to extinction could be a consequence of the mutation rate trajectory on which the symbiont embarked early on in its evolutionary history.
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Affiliation(s)
- Jon Bohlin
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Production Animals, Faculty of Veterinary Medicine, Norwegian University of Life Science, Oslo, Norway
| | - Brittany Rose
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ola Brynildsrud
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Production Animals, Faculty of Veterinary Medicine, Norwegian University of Life Science, Oslo, Norway
| | - Birgitte Freiesleben De Blasio
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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Epidemiology of Nucleus-Dwelling Holospora: Infection, Transmission, Adaptation, and Interaction with Paramecium. Results Probl Cell Differ 2020; 69:105-135. [PMID: 33263870 DOI: 10.1007/978-3-030-51849-3_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The chapter describes the exceptional symbiotic associations formed between the ciliate Paramecium and Holospora, highly infectious bacteria residing in the host nuclei. Holospora and Holospora-like bacteria (Alphaproteobacteria) are characterized by their ability for vertical and horizontal transmission in host populations, a complex biphasic life cycle, and pronounced preference for host species and colonized cell compartment. These bacteria are obligate intracellular parasites; thus, their metabolic repertoire is dramatically reduced. Nevertheless, they perform complex interactions with the host ciliate. We review ongoing efforts to unravel the molecular adaptations of these bacteria to their unusual lifestyle and the host's employment in the symbiosis. Furthermore, we summarize current knowledge on the genetic and genomic background of Paramecium-Holospora symbiosis and provide insights into the ecological and evolutionary consequences of this interaction. The diversity and occurrence of symbioses between ciliates and Holospora-like bacteria in nature is discussed in connection with transmission modes of symbionts, host specificity and compatibility of the partners. We aim to summarize 50 years of research devoted to these symbiotic systems and conclude trying to predict some perspectives for further studies.
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Renoz F, Pons I, Hance T. Evolutionary responses of mutualistic insect-bacterial symbioses in a world of fluctuating temperatures. CURRENT OPINION IN INSECT SCIENCE 2019; 35:20-26. [PMID: 31302355 DOI: 10.1016/j.cois.2019.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/29/2019] [Accepted: 06/20/2019] [Indexed: 06/10/2023]
Abstract
Climate change is altering the abundance and distribution of millions of insect species around the world and is a major contributor to the decline of numerous species. Many insect species may be indirectly affected through their nutritional dependence on mutualistic bacteria. Indeed, these bacterial partners generally have a highly reduced and static genome, resulting from millions of years of coevolution and isolation in insect cells, and have limited adaptive capacity. The dependence of insects on bacterial partners with narrow environmental tolerance also restricts their ability to adapt, potentially increasing the risk of their extinction, particularly in a world characterized by increasing and fluctuating temperatures. In this review, we examine how climate change can affect the evolutionary trajectories of bacterial mutualism in insects by considering the possible alternatives that may compensate for the dependence on bacterial partners that have become 'Achilles' heels'. We also discuss the beneficial and compensatory effects, as well as the antagonistic effects associated with so-called facultative symbionts in the context of an increased incidence of transient extreme temperatures.
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Affiliation(s)
- François Renoz
- Université catholique de Louvain, Earth and Life Institute, Biodiversity Research Center, Croix de Sud 4-5, bte L7.07.04, 1348 Louvain-la-Neuve, Belgium.
| | - Inès Pons
- Université catholique de Louvain, Earth and Life Institute, Biodiversity Research Center, Croix de Sud 4-5, bte L7.07.04, 1348 Louvain-la-Neuve, Belgium
| | - Thierry Hance
- Université catholique de Louvain, Earth and Life Institute, Biodiversity Research Center, Croix de Sud 4-5, bte L7.07.04, 1348 Louvain-la-Neuve, Belgium
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Bennett GM, Mao M. Comparative genomics of a quadripartite symbiosis in a planthopper host reveals the origins and rearranged nutritional responsibilities of anciently diverged bacterial lineages. Environ Microbiol 2018; 20:4461-4472. [PMID: 30047196 DOI: 10.1111/1462-2920.14367] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/15/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
Insects in the Auchenorrhyncha (Hemiptera: Suborder) established nutritional symbioses with bacteria approximately 300 million years ago (MYA). The suborder split early during its diversification (~ 250 MYA) into the Fulgoroidea (planthoppers) and Cicadomorpha (leafhoppers and cicadas). The two lineages share some symbionts, including Sulcia and possibly a Betaproteobacteria that collaboratively provide their hosts with 10 essential amino acids (EAA). Some hosts harbour three bacteria, as is common among planthoppers. However, genomic studies are currently restricted to the dual-bacterial symbioses found in Cicadomorpha, leaving the origins and functions of these more complex symbioses unclear. To address these questions, we sequenced the genomes and performed phylogenomic analyses of 'Candidatus Sulcia muelleri' (Bacteroidetes), 'Ca. Vidania fulgoroideae' (Betaproteobacteria) and 'Ca. Purcelliella pentastirinorum' (Gammaproteobacteria) from a planthopper (Cixiidae: Oliarus). In contrast to the Cicadomorpha, nutritional synthesis responsibilities are rearranged between the cixiid symbionts. Although Sulcia has a highly conserved genome across the Auchenorrhyncha, in the cixiids it is greatly reduced and provides only three EAAs. Vidania contributes the remaining seven EAAs. Phylogenomic results suggest that it represents an ancient symbiont lineage paired with Sulcia throughout the Auchenorrhyncha. Finally, Purcelliella was recently acquired from plant-insect associated bacteria (Pantoea-Erwinia) to provide B vitamins and metabolic support to its degenerate partners.
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Affiliation(s)
- Gordon M Bennett
- Life and Environmental Sciences Unit, University of California, Merced, CA, 95343, USA.,Department of Plant and Environmental Protections Sciences, University of Hawaii at Mānoa, Honolulu, HI, 96822, USA
| | - Meng Mao
- Life and Environmental Sciences Unit, University of California, Merced, CA, 95343, USA.,Department of Plant and Environmental Protections Sciences, University of Hawaii at Mānoa, Honolulu, HI, 96822, USA
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Abstract
Current understanding of many animal-microbial symbioses involving unculturable bacterial symbionts with much-reduced genomes derives almost entirely from nonquantitative inferences from genome data. To overcome this limitation, we reconstructed multipartner metabolic models that quantify both the metabolic fluxes within and between three xylem-feeding insects and their bacterial symbionts. This revealed near-complete metabolic segregation between cooccurring bacterial symbionts, despite extensive metabolite exchange between each symbiont and the host, suggestive of strict host controls over the metabolism of its symbionts. We extended the model analysis to investigate metabolic costs. The positive relationship between symbiont genome size and the metabolic cost incurred by the host points to fitness benefits to the host of bearing symbionts with small genomes. The multicompartment metabolic models developed here can be applied to other symbioses that are not readily tractable to experimental approaches. Various intracellular bacterial symbionts that provide their host with essential nutrients have much-reduced genomes, attributed largely to genomic decay and relaxed selection. To obtain quantitative estimates of the metabolic function of these bacteria, we reconstructed genome- and transcriptome-informed metabolic models of three xylem-feeding insects that bear two bacterial symbionts with complementary metabolic functions: a primary symbiont, Sulcia, that has codiversified with the insects, and a coprimary symbiont of distinct taxonomic origin and with different degrees of genome reduction in each insect species (Hodgkinia in a cicada, Baumannia in a sharpshooter, and Sodalis in a spittlebug). Our simulations reveal extensive bidirectional flux of multiple metabolites between each symbiont and the host, but near-complete metabolic segregation (i.e., near absence of metabolic cross-feeding) between the two symbionts, a likely mode of host control over symbiont metabolism. Genome reduction of the symbionts is associated with an increased number of host metabolic inputs to the symbiont and also reduced metabolic cost to the host. In particular, Sulcia and Hodgkinia with genomes of ≤0.3 Mb are calculated to recycle ∼30 to 80% of host-derived nitrogen to essential amino acids returned to the host, while Baumannia and Sodalis with genomes of ≥0.6 Mb recycle 10 to 15% of host nitrogen. We hypothesize that genome reduction of symbionts may be driven by selection for increased host control and reduced host costs, as well as by the stochastic process of genomic decay and relaxed selection.
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Abstract
Cicadas are dependent on the essential bacterial symbionts Sulcia and Hodgkinia. The symbiont genomes are extremely streamlined for provisioning of essential amino acids and other nutrients. In some cicada lineages, Hodgkinia genomes are fragmented into numerous minicircles, which may represent a critical stage of genomic erosion close to collapse. What would happen subsequently? Our survey of the Japanese cicada diversity revealed that while Sulcia is conserved among all species, the majority of them have lost Hodgkinia and instead harbor yeast-like fungal associates. The fungal symbionts are phylogenetically intermingled with cicada-parasitizing Ophiocordyceps fungi, indicating recurrent symbiont replacements by entomopathogens in cicadas and providing insights into the mechanisms underlying the parasitism-symbiosis evolutionary continuum, compensation of symbiont genome erosion, and diversification of host-symbiont associations. Diverse insects are associated with ancient bacterial symbionts, whose genomes have often suffered drastic reduction and degeneration. In extreme cases, such symbiont genomes seem almost unable to sustain the basic cellular functioning, which comprises an open question in the evolution of symbiosis. Here, we report an insect group wherein an ancient symbiont lineage suffering massive genome erosion has experienced recurrent extinction and replacement by host-associated pathogenic microbes. Cicadas are associated with the ancient bacterial co-obligate symbionts Sulcia and Hodgkinia, whose streamlined genomes are specialized for synthesizing essential amino acids, thereby enabling the host to live on plant sap. However, our inspection of 24 Japanese cicada species revealed that while all species possessed Sulcia, only nine species retained Hodgkinia, and their genomes exhibited substantial structural instability. The remaining 15 species lacked Hodgkinia and instead harbored yeast-like fungal symbionts. Detailed phylogenetic analyses uncovered repeated Hodgkinia-fungus and fungus-fungus replacements in cicadas. The fungal symbionts were phylogenetically intermingled with cicada-parasitizing Ophiocordyceps fungi, identifying entomopathogenic origins of the fungal symbionts. Most fungal symbionts of cicadas were uncultivable, but the fungal symbiont of Meimuna opalifera was cultivable, possibly because it is at an early stage of fungal symbiont replacement. Genome sequencing of the fungal symbiont revealed its metabolic versatility, presumably capable of synthesizing almost all amino acids, vitamins, and other metabolites, which is more than sufficient to compensate for the Hodgkinia loss. These findings highlight a straightforward ecological and evolutionary connection between parasitism and symbiosis, which may provide an evolutionary trajectory to renovate deteriorated ancient symbiosis via pathogen domestication.
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Martínez-Cano DJ, Bor G, Moya A, Delaye L. Testing the Domino Theory of Gene Loss in Buchnera aphidicola: The Relevance of Epistatic Interactions. Life (Basel) 2018; 8:life8020017. [PMID: 29843462 PMCID: PMC6027505 DOI: 10.3390/life8020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 02/07/2023] Open
Abstract
The domino theory of gene loss states that when some particular gene loses its function and cripples a cellular function, selection will relax in all functionally related genes, which may allow for the non-functionalization and loss of these genes. Here we study the role of epistasis in determining the pattern of gene losses in a set of genes participating in cell envelope biogenesis in the endosymbiotic bacteria Buchnera aphidicola. We provide statistical evidence indicating pairs of genes in B. aphidicola showing correlated gene loss tend to have orthologs in Escherichia coli known to have alleviating epistasis. In contrast, pairs of genes in B. aphidicola not showing correlated gene loss tend to have orthologs in E. coli known to have aggravating epistasis. These results suggest that during the process of genome reduction in B. aphidicola by gene loss, positive or alleviating epistasis facilitates correlated gene losses while negative or aggravating epistasis impairs correlated gene losses. We interpret this as evidence that the reduced proteome of B. aphidicola contains less pathway redundancy and more compensatory interactions, mimicking the situation of E. coli when grown under environmental constrains.
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Affiliation(s)
- David J Martínez-Cano
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico.
| | - Gil Bor
- CIMAT, A.P. 402, Guanajuato 36000, Gto., Mexico.
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, Avenida de Catalunya 21, 46020 València, Spain.
- Institute for Integrative Systems Biology, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain.
| | - Luis Delaye
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico.
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