scholarly journals Associations between depth and micro-diversity within marine viral communities revealed through metagenomics

2019 ◽  
Author(s):  
FH Coutinho ◽  
R Rosselli ◽  
F Rodríguez-Valera
Keyword(s):  
Marine Ecosystems ◽  
Replication Proteins ◽  
Synonymous Mutations ◽  
Genes Encoding ◽  
Marine Viruses ◽  
Viral Communities ◽  
Depth Gradients ◽  
Seawater Samples ◽  
Biological Entities ◽  
Bathypelagic Zone

AbstractViruses are extremely abundant and diverse biological entities that contribute to the functioning of marine ecosystems. Despite their recognized importance no studies have addressed trends of micro-diversity in marine viral communities across depth gradients. To fill this gap we obtained metagenomes from both the cellular and viral fractions of Mediterranean seawater samples spanning the epipelagic to the bathypelagic zone at 15, 45, 60 and 2000 meters deep. The majority of viral genomic sequences obtained were derived from bacteriophages of the order Caudovirales, and putative host assignments suggested that they infect some of the most abundant bacteria in marine ecosystems such as Pelagibacter, Puniceispirillum and Prochlorococcus. We evaluated micro-diversity patterns by measuring the accumulation of synonymous and non-synonymous mutations in viral genes. Our results demonstrated that the degree of micro-diversity differs among genes encoding metabolic, structural, and replication proteins and that the degree of micro-diversity increased with depth. These trends of micro-diversity were linked to the changes in environmental conditions observed throughout the depth gradient, such as energy availability, host densities and proportion of actively replicating viruses. These observations allowed us to generate hypotheses regarding the selective pressures acting upon marine viruses from the epipelagic to the bathypelagic zones.

scholarly journals Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the Mediterranean

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Felipe Hernandes Coutinho ◽  
Riccardo Rosselli ◽  
Francisco Rodríguez-Valera
Keyword(s):  
Real Life ◽  
Host Density ◽  
Marine Ecosystems ◽  
Microbial Evolution ◽  
Evolutionary Strategies ◽  
Host Recognition ◽  
Replication Proteins ◽  
Viral Genes ◽  
Viral Communities ◽  
Depth Gradients

ABSTRACT The evolutionary interactions between viruses and their prokaryotic hosts remain a little-known aspect of microbial evolution. Most studies on this topic were carried out in pure cultures that challenge one virus with one bacterial clone at a time, which is very removed from real-life situations. Few studies have addressed trends of microdiversity in marine viral communities throughout depth gradients. We analyzed metagenomes from both the cellular and viral fractions of Mediterranean seawater samples spanning the epipelagic to the bathypelagic zones at depths of 15, 45, 60, and 2,000 m during the summer stratification of the water column. We evaluated microdiversity patterns by measuring the accumulation of synonymous and nonsynonymous mutations in viral genes. Our results demonstrated clear depth-dependent trends in the frequency of polymorphic sites and nonsynonymous mutations among genes encoding metabolic, structural, and replication proteins. These differences were linked to changes in energy availability, host and viral densities, and the proportions of actively replicating viruses. We propose the hypothesis that in the energy-rich, high-host-density, euphotic depths, selection acts to favor diversity of the host recognition machinery to increase host range, while in energy-depleted aphotic waters, selection acts on viral replication fitness, enhancing diversity in auxiliary metabolic genes. IMPORTANCE Viruses are extremely abundant and diverse biological entities that contribute to the functioning of marine ecosystems. Despite their recognized importance, few studies have addressed trends of mutation accumulation in marine viral communities across depth gradients. By investigating these trends, we show that mutation frequencies differ among viral genes according to their molecular functions, with the highest microdiversity occurring among proteins related to host metabolism, followed by structural proteins and, lastly, genome replication proteins. This is in agreement with evolutionary theory that postulates that housekeeping genes are under strong purifying selection. We also observed a positive association between depth and microdiversity. One exception to this trend was the host recognition proteins from the deep chlorophyll maximum, which displayed strikingly high microdiversity, which we hypothesize to be associated with intraspecies competition for hosts. Finally, our data allowed us to propose a theoretical model for viral microdiversity across the depth gradient. These discoveries are of special relevance because many of the viral genomic sequences discovered here were predicted to infect some of the most abundant bacteria in marine ecosystems, such as “Candidatus Pelagibacter,” Puniceispirillum, and Prochlorococcus.

scholarly journals Essential Role for NFI-C/CTF Transcription-Replication Factor in Tooth Root Development

2003 ◽  
Vol 23 (3) ◽  
pp. 1075-1084 ◽  
Author(s):  
George Steele-Perkins ◽  
Kenneth G. Butz ◽  
Gary E. Lyons ◽  
Margarita Zeichner-David ◽  
Heung-Joong Kim ◽  
...  
Keyword(s):  
Root Development ◽  
Tooth Development ◽  
Physiological Role ◽  
Premature Death ◽  
Tooth Root ◽  
Replication Proteins ◽  
Wild Type ◽  
Organ Systems ◽  
Genes Encoding ◽  
Nuclear Factor I

ABSTRACT The mammalian tooth forms by a series of reciprocal epithelial-mesenchymal interactions. Although several signaling pathways and transcription factors have been implicated in regulating molar crown development, relatively little is known about the regulation of root development. Four genes encoding nuclear factor I (NFI) transcription-replication proteins are present in the mouse genome: Nfia, Nfib, Nfic, and Nfix. In order to elucidate its physiological role(s), we disrupted the Nfic gene in mice. Heterozygous animals appear normal, whereas Nfic−/− mice have unique tooth pathologies: molars lacking roots, thin and brittle mandibular incisors, and weakened abnormal maxillary incisors. Feeding in Nfic−/− mice is impaired, resulting in severe runting and premature death of mice reared on standard laboratory chow. However, a soft-dough diet mitigates the feeding impairment and maintains viability. Although Nfic is expressed in many organ systems, including the developing tooth, the tooth root development defects were the prominent phenotype. Indeed, molar crown development is normal, and well-nourished Nfic−/− animals are fertile and can live as long as their wild-type littermates. The Nfic mutation is the first mutation described that affects primarily tooth root formation and should greatly aid our understanding of postnatal tooth development.

scholarly journals Minimization of energy transduction confers resistance to phosphine in the rice weevil, Sitophilus oryzae

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kyeongnam Kim ◽  
Jeong Oh Yang ◽  
Jae-Yoon Sung ◽  
Ji-Young Lee ◽  
Jeong Sun Park ◽  
...  
Keyword(s):  
Cancer Metabolism ◽  
Insect Pests ◽  
Sitophilus Oryzae ◽  
Resistance Mechanism ◽  
Energy Transduction ◽  
Metabolic Reprogramming ◽  
Rice Weevil ◽  
Altered Expression ◽  
Synonymous Mutations ◽  
Genes Encoding

Abstract Infestation of phosphine (PH3) resistant insects threatens global grain reserves. PH3 fumigation controls rice weevil (Sitophilus oryzae) but not highly resistant insect pests. Here, we investigated naturally occurring strains of S. oryzae that were moderately resistant (MR), strongly resistant (SR), or susceptible (wild-type; WT) to PH3 using global proteome analysis and mitochondrial DNA sequencing. Both PH3 resistant (PH3–R) strains exhibited higher susceptibility to ethyl formate-mediated inhibition of cytochrome c oxidase than the WT strain, whereas the disinfectant PH3 concentration time of the SR strain was much longer than that of the MR strain. Unlike the MR strain, which showed altered expression levels of genes encoding metabolic enzymes involved in catabolic pathways that minimize metabolic burden, the SR strain showed changes in the mitochondrial respiratory chain. Our results suggest that the acquisition of strong PH3 resistance necessitates the avoidance of oxidative phosphorylation through the accumulation of a few non-synonymous mutations in mitochondrial genes encoding complex I subunits as well as nuclear genes encoding dihydrolipoamide dehydrogenase, concomitant with metabolic reprogramming, a recognized hallmark of cancer metabolism. Taken together, our data suggest that reprogrammed metabolism represents a survival strategy of SR insect pests for the compensation of minimized energy transduction under anoxic conditions. Therefore, understanding the resistance mechanism of PH3–R strains will support the development of new strategies to control insect pests.

scholarly journals The role of synonymous mutations in the evolution of TEM β-lactamase genes

2021 ◽  
Author(s):  
Mohammad Faheem ◽  
Charles J. Zhang ◽  
Monica N. Morris ◽  
Juergen Pleiss ◽  
Peter Oelschlaeger
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Disc Diffusion ◽  
Nucleotide Change ◽  
Nonsynonymous Mutation ◽  
Synonymous Mutations ◽  
Extended Spectrum ◽  
Genes Encoding ◽  
Variant Genes

Nonsynonymous mutations are well documented in TEM β-lactamases. The resulting amino acid changes often alter the conferred phenotype from broad spectrum (2b) conferred by TEM-1 to extended spectrum (2be), inhibitor resistant (2br), or both extended spectrum and inhibitor resistant (2ber). The encoding blaTEM genes also deviate in numerous synonymous mutations, which are not well understood. blaTEM-3 (2be), blaTEM-33 (2br), and blaTEM-109 (2ber) were studied in comparison to blaTEM-1. blaTEM-33 was chosen for more detailed studies, because it deviates from blaTEM-1 by a single nonsynonymous mutation and three additional, synonymous mutations. Genes encoding the enzymes with only nonsynonymous or all, including synonymous, mutations plus all permutations between blaTEM-1 and blaTEM-33 were expressed in Escherichia coli cells. In disc diffusion assays, genes encoding TEM-3, TEM-33, and TEM-109 with all synonymous mutations resulted in higher resistance levels than genes without synonymous mutations. Disc diffusion assays with the 16 genes carrying all possible nucleotide change combinations between blaTEM-1 and blaTEM-33 indicated different susceptibilities for different variants. Nucleotide BLAST searches did not identify genes without synonymous mutations but some without nonsynonymous mutations. Energies of possible secondary mRNA structures calculated with mfold are generally higher with synonymous mutations, suggesting that their role could be to destabilize the mRNA and facilitate its unfolding for efficient translation. In summary, our data indicate that transitions from blaTEM-1 to other variant genes by simply acquiring the nonsynonymous mutations is not favored. Instead, synonymous mutations seem to support the transition to other variant genes with nonsynonymous mutations leading to different phenotypes.

scholarly journals Divergent mitochondrial and nuclear OXPHOS genes are candidates for genetic incompatibilities inFicedulaFlycatchers

2019 ◽  
Author(s):  
Eva van der heijden ◽  
S. Eryn McFarlane ◽  
Tom van der Valk ◽  
Anna Qvarnström
Keyword(s):  
Energy Metabolism ◽  
Nuclear Dna ◽  
Resting Metabolic Rate ◽  
Population Expansion ◽  
Nuclear Genes ◽  
F1 Hybrids ◽  
Relative Role ◽  
Synonymous Mutations ◽  
Genes Encoding ◽  
Hybrid Dysfunction

AbstractHybrid dysfunction is an important source of reproductive isolation between emerging species. Bateson-Dobzhansky-Muller incompatibilities are theoretically well-recognized as the underlying cause of low hybrid dysfunction. However, especially in wild populations, little empirical evidence exists for which genes are involved in such incompatibilities. The relative role of ecological divergence in causing the build-up of genetic incompatibilities in relation to other processes such as genomic conflict therefore remains largely unknown. Genes involved in energy metabolism are potential candidates for genetic incompatibilities, since energy metabolism depends on co-expression of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) leading to mitonuclear coadaptation. When mitochondrial and nuclear genes lacking a co-evolutionary history appear together in hybrids, incompatibilities could arise.Ficedulaflycatcher F1 hybrids have a higher resting metabolic rate (RMR) compared to the parental species, which could be a sign of genetic incompatibilities between energy metabolism genes that diverged in response to environmental differences while the species were in allopatry. Based on sequences of 15 mitochondrial genes of 264 individuals, we show that the two species have divergent mtDNA caused by the build-up of mainly synonymous mutations and a few non-synonymous mutations. Pied flycatcher mitogenomes show evidence of non-neutrality, indicating a selective sweep or population expansion. There is little variation in the nuclear OXPHOS-related proteins and no significant deviation from neutrality, however, specific codon identified sites might be under positive selection in both mitochondrial and nuclear genes encoding OXPHOS proteins for complex I and III. Taken together, these diverged mitonuclear genes therefore constitute possible candidates underlying, at least part of the genetic incompatibilities that cause hybrid dysfunction in crosses between collared and pied flycatchers.

scholarly journals Rising through the Ranks: Seasonal and Diel Patterns of Marine Viruses

2020 ◽  
Author(s):  
Gur Hevroni ◽  
José Flores-Uribe ◽  
Oded Béjà ◽  
Alon Philosof
Keyword(s):  
High Throughput Sequencing ◽  
Seasonal Succession ◽  
Nucleotide Composition ◽  
Potential Interaction ◽  
Molecular Techniques ◽  
Model Systems ◽  
Marine Viruses ◽  
Viral Communities ◽  
Microbe Interactions ◽  
Changes Over Time

Virus-microbe interactions have been studied in great molecular details for many years in cultured model systems, yielding a plethora of knowledge on how viruses use and manipulate host machinery. Since the advent of molecular techniques and high-throughput sequencing, viruses have been deemed the most abundant organisms on earth and methods such as co-occurrence, nucleotide composition and other statistical frameworks have been widely used to infer virus-microbe interactions, overcoming the limitations of culturing methods. However, their accuracy and relevance is still debatable, as co-occurrence does not necessarily mean interaction. Here, we introduce an ecological perspective of marine viral communities and potential interaction with their hosts, using analyses that make no prior assumptions on specific virus-host pairs. By size fractioning water samples into "free viruses" and "microbes" (i.e. also viruses inside or attached to their hosts) and looking at how viral groups abundance changes over time along both fractions, we show that the viral community is undergoing a change in rank abundance across seasons, suggesting a seasonal succession of viruses in the Red Sea. We use abundance patterns in the different size fractions to classify viral populations, indicating potential diverse interactions with their hosts and potential differences in life history traits between major viral groups. Finally, we show hourly resolved variations of intracellular abundance of similar viral groups, which might indicate differences in their infection cycles or metabolic capacities.

scholarly journals Ecological roles of the parasitic phytomyxids (plasmodiophorids) in marine ecosystems - a review

2011 ◽  
Vol 62 (4) ◽  
pp. 365 ◽  
Author(s):  
Sigrid Neuhauser ◽  
Martin Kirchmair ◽  
Frank H. Gleason
Keyword(s):  
Organic Matter ◽  
Reproductive Success ◽  
Food Webs ◽  
Marine Ecosystems ◽  
Freshwater Ecosystems ◽  
Marine Biodiversity ◽  
Microbial Food Webs ◽  
Marine Habitats ◽  
Ecological Roles ◽  
Marine Viruses

Phytomyxea (plasmodiophorids) is an enigmatic group of obligate biotrophic parasites. Most of the known 41 species are associated with terrestrial and freshwater ecosystems. However, the potential of phytomyxean species to influence marine ecosystems either directly by causing diseases of their hosts or indirectly as vectors of viruses is enormous, although still unexplored. In all, 20% of the currently described phytomyxean species are parasites of some of the key primary producers in the ocean, such as seagrasses, brown algae and diatoms; however, information on their distribution, abundance and biodiversity is either incomplete or lacking. Phytomyxean species influence fitness by altering the metabolism and/or the reproductive success of their hosts. The resulting changes can (1) have an impact on the biodiversity within host populations, and (2) influence microbial food webs because of altered availability of nutrients (e.g. changed metabolic status of host, transfer of organic matter). Also, phytomyxean species may affect their host populations indirectly by transmitting viruses. The majority of the currently known single-stranded RNA marine viruses structurally resemble the viruses transmitted by phytomyxean species to crops in agricultural environments. Here, we explore possible ecological roles of these parasites in marine habitats; however, only the inclusion of Phytomyxea in marine biodiversity studies will allow estimation of the true impact of these species on global primary production in the oceans.

scholarly journals Viral serine palmitoyltransferase induces metabolic switch in sphingolipid biosynthesis and is required for infection of a marine alga

2016 ◽  
Vol 113 (13) ◽  
pp. E1907-E1916 ◽  
Author(s):  
Carmit Ziv ◽  
Sergey Malitsky ◽  
Alaa Othman ◽  
Shifra Ben-Dor ◽  
Yu Wei ◽  
...  
Keyword(s):  
De Novo ◽  
Serine Palmitoyltransferase ◽  
Metabolic Switch ◽  
Marine Viruses ◽  
Key Enzyme ◽  
Infected Cells ◽  
Biochemical Analyses ◽  
Biological Entities ◽  
Sphingolipid Biosynthesis

Marine viruses are the most abundant biological entities in the oceans shaping community structure and nutrient cycling. The interaction between the bloom-forming algaEmiliania huxleyiand its specific large dsDNA virus (EhV) is a major factor determining the fate of carbon in the ocean, thus serving as a key host-pathogen model system. The EhV genome encodes for a set of genes involved in the de novo sphingolipid biosynthesis, not reported in any viral genome to date. We combined detailed lipidomic and biochemical analyses to characterize the functional role of this virus-encoded pathway during lytic viral infection. We identified a major metabolic shift, mediated by differential substrate specificity of virus-encoded serine palmitoyltransferase, a key enzyme of sphingolipid biosynthesis. Consequently, unique viral glycosphingolipids, composed of unusual hydroxylated C17 sphingoid bases (t17:0) were highly enriched in the infected cells, and their synthesis was found to be essential for viral assembly. These findings uncover the biochemical bases of the virus-induced metabolic rewiring of the host sphingolipid biosynthesis during the chemical “arms race” in the ocean.

scholarly journals Marine Viruses: Key Players in Marine Ecosystems

Viruses ◽  
2017 ◽  
Vol 9 (10) ◽  
pp. 302 ◽  
Author(s):  
Mathias Middelboe ◽  
Corina Brussaard
Keyword(s):  
Marine Ecosystems ◽  
Key Players ◽  
Marine Viruses
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