Genome Reduction Research Articles

Reducción de la Dimensionalidad en Perfiles Tumorales con Metodos de Kernel y Redes Neuronales

Los perfiles tumorales en humanos pueden ser caracterizados por su genómica mediante la expresión de miles de genes. Este tipo de señales pueden ser aprovechadas para detectar estadísticamente patrones que permitan clasificar o agrupar de manera supervisada o no supervisada perfiles tumorales según su fenotipo. En esta presentación y revisión se busca listar dos casos para poder reducir la dimensionalidad genómica y encontrar biomarcadores que permitan realizar las tareas de aprendizaje estadístico mencionadas. Para reducir la dimensionalidad se utilizan funciones de Kernel en combinación con redes Neuronales Artificiales. Los resultados obtenidos en la presente revisión muestran el potencial de estas herramientas para el procesamiento de datos genómicos en pacientes oncológicos.

Synthetic biology as a technoscience: The case of minimal genomes and essential genes

This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific organisms towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature?Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience.

The Transfer of the Ferredoxin Gene From the Chloroplast to the Nuclear Genome Is Ancient Within the Paraphyletic Genus Thalassiosira.

Ferredoxins are iron–sulfur proteins essential for a wide range of organisms because they are an electron transfer mediator involved in multiple metabolic pathways. In phytoplankton, these proteins are active in the mature chloroplasts, but the petF gene, encoding for ferredoxin, has been found either to be in the chloroplast genome or transferred to the nuclear genome as observed in the green algae and higher plant lineage. We experimentally determined the location of the petF gene in 12 strains of Thalassiosira covering three species using DNA sequencing and qPCR assays. The results showed that petF gene is located in the nuclear genome of all confirmed Thalassiosira oceanica strains (CCMP0999, 1001, 1005, and 1006) tested. In contrast, all Thalassiosira pseudonana (CCMP1012, 1013, 1014, and 1335) and Thalassiosira weissflogii (CCMP1010, 1049, and 1052) strains studied retained the gene in the chloroplast genome, as generally observed for Bacillariophyceae. Our evolutionary analyses further extend the dataset on the localization of the petF gene in the Thalassiosirales. The realization that the petF gene is nuclear-encoded in the Skeletonema genus allowed us to trace the petF gene transfer back to a single event that occurred within the paraphyletic genus Thalassiosira. Phylogenetic analyses revealed the need to reassess the taxonomic assignment of the Thalassiosira strain CCMP1616, since the genes used in our study did not cluster within the T. oceanica lineage. Our results suggest that this strains’ diversification occurred prior to the ferredoxin gene transfer event. The functional transfer of petF genes provides insight into the evolutionary processes leading to chloroplast genome reduction and suggests ecological adaptation as a driving force for such chloroplast to nuclear gene transfer.

Genome-Wide Duplication of Allotetraploid Brassica napus Produces Novel Characteristics and Extensive Ploidy Variation in Self-Pollinated Progeny.

Whole genome duplications (WGDs) have played a major role in angiosperm species evolution. Polyploid plants have undergone multiple cycles of ancient WGD events during their evolutionary history. However, little attention has been paid to the additional WGD of the existing allopolyploids. In this study, we explored the influences of additional WGD on the allopolyploid Brassica napus. Compared to tetraploid B. napus, octoploid B. napus (AAAACCCC, 2n = 8x =76) showed significant differences in phenotype, reproductive ability and the ploidy of self-pollinated progeny. Genome duplication also altered a key reproductive organ feature in B. napus, that is, increased the number of pollen apertures. Unlike autopolyploids produced from the diploid Brassica species, the octoploid B. napus produced from allotetraploid B. napus had a relatively stable meiotic process, high pollen viability and moderate fertility under self-pollination conditions, indicating that sub-genomic interactions may be important for the successful establishment of higher-order polyploids. Doubling the genome of B. napus provided us with an opportunity to gain insight into the flexibility of the Brassica genomes. The genome size of self-pollinated progeny of octoploid B. napus varied greatly, and was accompanied by extensive genomic instability, such as aneuploidy, mixed-ploidy and mitotic abnormality. The octoploid B. napus could go through any of genome reduction, equilibrium or expansion in the short-term, thus providing a novel karyotype library for the Brassica genus. Our results reveal the short-term evolutionary consequences of recurrent polyploidization events, and help to deepen our understanding of polyploid plant evolution.

Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells

BackgroundPathogenic Rickettsia species belonging to the spotted fever group are arthropod-borne, obligate intracellular bacteria which exhibit preferential tropism for host microvascular endothelium in the mammalian hosts, resulting in disease manifestations attributed primarily to endothelial damage or dysfunction. Although rickettsiae are known to undergo evolution through genomic reduction, the mechanisms by which these pathogens regulate their transcriptome to ensure survival in tick vectors and maintenance by transovarial/transstadial transmission, in contrast to their ability to cause debilitating infections in human hosts remain unknown. In this study, we compare the expression profiles of rickettsial sRNAome/transcriptome and determine the transcriptional start sites (TSSs) of R. conorii transcripts during in vitro infection of human and tick host cells.ResultsWe performed deep sequencing on total RNA from Amblyomma americanum AAE2 cells and human microvascular endothelial cells (HMECs) infected with R. conorii. Strand-specific RNA sequencing of R. conorii transcripts revealed the expression 32 small RNAs (Rc_sR’s), which were preferentially expressed above the limit of detection during tick cell infection, and confirmed the expression of Rc_sR61, sR71, and sR74 by quantitative RT-PCR. Intriguingly, a total of 305 and 132 R. conorii coding genes were differentially upregulated (> 2-fold) in AAE2 cells and HMECs, respectively. Further, enrichment for primary transcripts by treatment with Terminator 5′-Phosphate-dependent Exonuclease resulted in the identification of 3903 and 2555 transcription start sites (TSSs), including 214 and 181 primary TSSs in R. conorii during the infection to tick and human host cells, respectively. Seventy-five coding genes exhibited different TSSs depending on the host environment. Finally, we also observed differential expression of 6S RNA during host-pathogen and vector-pathogen interactions in vitro, implicating an important role for this noncoding RNA in the regulation of rickettsial transcriptome depending on the supportive host niche.ConclusionsIn sum, the findings of this study authenticate the presence of novel Rc_sR’s in R. conorii, reveal the first evidence for differential expression of coding transcripts and utilization of alternate transcriptional start sites depending on the host niche, and implicate a role for 6S RNA in the regulation of coding transcriptome during tripartite host-pathogen-vector interactions.

Genome reduction enhances production of polyhydroxyalkanoate and alginate oligosaccharide in Pseudomonas mendocina

Pseudomonas mendocina NK-01 previously isolated by our lab is able to accumulate medium-chain-length polyhydroxyalkanoate (mcl-PHA) intracellularly and secrete alginate oligosaccharide (AO) to the extracellular milieu. The present study aimed at investigating whether improved production of mcl-PHA and AO by P. mendocina can be accomplished by genome reduction. In this study, 14 large genomic fragments accounting for 7.7% of the genome of P. mendocina NK-01 were sequentially deleted to generate a series of genome-reduced strains by an upp-based markerless knockout method. As a result, the intracellular ATP/ADP ratio of the strain NKU421 with the largest deletion improved by 11 times compared to NK-01. More importantly, the mcl-PHA and AO yields of NKU421 increased by 114.8% and 27.8%, respectively. Enhancing mcl-PHA and AO production by NKU421 may be attributed to improved transcriptional levels of PHA synthase genes and AO secretion-related genes. The present study suggests that rational reduction of bacterial genome is a feasible approach to construct an optimal chassis for enhanced production of bacterial metabolites. In the future, further reduction of the NKU421 genome can be expected to create high-performance chassis for the development of microbial cell factories.

I have a kit and I create worlds: synthetic ecology from synthetic genomes

The genome is the blueprint for life. A genome sequence can be transcribed and translated by molecular machines to assemble an organism capable of replication, sensation, and response. Organisms respond to each other, forming intricate interaction webs that manifest as ecosystems, defining the world we live in and rely on. It all starts with a genome. And if we can build a genome, we can create worlds. This article is protected by copyright. All rights reserved.

Comparative Plastid Genomics of Non-Photosynthetic Chrysophytes: Genome Reduction and Compaction.

Spumella-like heterotrophic chrysophytes are important eukaryotic microorganisms that feed on bacteria in aquatic and soil environments. They are characterized by their lack of pigmentation, naked cell surface, and extremely small size. Although Spumella-like chrysophytes have lost their photosynthetic ability, they still possess a leucoplast and retain a plastid genome. We have sequenced the plastid genomes of three non-photosynthetic chrysophytes, Spumella sp. Baeckdong012018B8, Pedospumella sp. Jangsampo120217C5 and Poteriospumella lacustris Yongseonkyo072317C3, and compared them to the previously sequenced plastid genome of “Spumella” sp. NIES-1846 and photosynthetic chrysophytes. We found the plastid genomes of Spumella-like flagellates to be generally conserved with respect to genome structure and housekeeping gene content. We nevertheless also observed lineage-specific gene rearrangements and duplication of partial gene fragments at the boundary of the inverted repeat and single copy regions. Most gene losses correspond to genes for proteins involved in photosynthesis and carbon fixation, except in the case of petF. The newly sequenced plastid genomes range from ~55.7 kbp to ~62.9 kbp in size and share a core set of 45 protein-coding genes, 3 rRNAs, and 32 to 34 tRNAs. Our results provide insight into the evolutionary history of organelle genomes via genome reduction and gene loss related to loss of photosynthesis in chrysophyte evolution.

Screening of a genome-reduced Corynebacterium glutamicum strain library for improved heterologous cutinase secretion.

The construction of microbial platform organisms by means of genome reduction is an ongoing topic in biotechnology. In this study, we investigated whether the deletion of single or multiple gene clusters has a positive effect on the secretion of cutinase from Fusarium solani pisi in the industrial workhorse Corynebacterium glutamicum. A total of 22 genome-reduced strain variants were compared applying two Sec signal peptides from Bacillus subtilis. High-throughput phenotyping using robotics-integrated microbioreactor technology with automated harvesting revealed distinct cutinase secretion performance for a specific combination of signal peptide and genomic deletions. The biomass-specific cutinase yield for strain GRS41_51_NprE was increased by~200%, although the growth rate was reduced by~60%. Importantly, the causative deletions of genomic clusters cg2801-cg2828 and rrnC-cg3298 could not have been inferred a priori. Strikingly, bioreactor fed-batch cultivations at controlled growth rates resulted in a complete reversal of the screening results, with the cutinase yield for strain GRS41_51_NprE dropping by~25% compared to the reference strain. Thus, the choice of bioprocess conditions may turn a 'high-performance' strain from batch screening into a 'low-performance' strain in fed-batch cultivation. In conclusion, future studies are needed in order to understand metabolic adaptations of C.glutamicum to both genomic deletions and different bioprocess conditions.

Is the evolution of carnivory connected with genome size reduction?

As repeatedly shown, the remarkable variation in the genome size of angiosperms can be shaped by extrinsic selective pressures, including nutrient availability. Carnivory has evolved independently in 10 angiosperm clades, but all carnivorous plants share a common affinity to nutrient-poor habitats. As such, carnivory and genome reduction could be responses to the same environmental pressure. Indeed, the smallest genomes among flowering plants are found in the carnivorous family Lentibulariaceae, where a unique mutation in cytochrome c oxidase (COX) is suspected to promote genome miniaturization. Despite these hypotheses, a phylogenetically informed test of genome size and nutrient availability across carnivorous clades has so far been missing. Using linear mixed models, we compared genome sizes of 127 carnivorous plants from 7 diverse angiosperm clades with 1072 of their noncarnivorous relatives. We also tested whether genome size in Lentibulariaceae reflects the presence of the COX mutation. The genome sizes of carnivorous plants do not differ significantly from those of their noncarnivorous relatives. Based on available data, no significant association between the COX mutation and genome miniaturization could be confirmed, not even when considering polyploidy. Carnivory alone does not seem to significantly affect genome size decrease. Plausibly, it might actually counterbalance the effect of nutrient limitation on genome size evolution. The role of the COX mutation in genome miniaturization needs to be evaluated by analysis of a broader data set because current knowledge of its presence across Lentibulariaceae covers less than 10% of the species diversity in this family.

Mycoavidus sp. Strain B2-EB: Comparative Genomics Reveals Minimal Genomic Features Required by a Cultivable Burkholderiaceae-Related Endofungal Bacterium.

Obligate bacterial endosymbionts are critical to the existence of many eukaryotes. Such endobacteria are usually characterized by reduced genomes and metabolic dependence on the host, which may cause difficulty in isolating them in pure cultures. Family Burkholderiaceae-related endofungal bacteria affiliated with the Mycoavidus-Glomeribacter clade can be associated with the fungal subphyla Mortierellomycotina and Glomeromycotina. In this study, a cultivable endosymbiotic bacterium, Mycoavidus sp. strain B2-EB, present in the fungal host Mortierella parvispora was obtained successfully. The B2-EB genome (1.88 Mb) represents the smallest genome among the endofungal bacterium Mycoavidus cysteinexigens (2.64-2.80 Mb) of Mortierella elongata and the uncultured endosymbiont "Candidatus Glomeribacter gigasporarum" (1.37 to 2.36 Mb) of arbuscular mycorrhizal fungi. Despite a reduction in genome size, strain B2-EB displays a high genome completeness, suggesting a nondegenerative reduction in the B2-EB genome. Compared with a large proportion of transposable elements (TEs) in other known Mycoavidus genomes (7.2 to 11.5% of the total genome length), TEs accounted for only 2.4% of the B2-EB genome. This pattern, together with a high proportion of single-copy genes in the B2-EB genome, suggests that the B2-EB genome reached a state of relative evolutionary stability. These results represent the most streamlined structure among the cultivable endofungal bacteria and suggest the minimal genome features required by both an endofungal lifestyle and artificial culture. This study allows us to understand the genome evolution of Burkholderiaceae-related endosymbionts and to elucidate microbiological interactions.IMPORTANCE This study attempted the isolation of a novel endobacterium, Mycoavidus sp. B2-EB (JCM 33615), harbored in the fungal host Mortierella parvispora E1425 (JCM 39028). We report the complete genome sequence of this strain, which possesses a reduced genome size with relatively high genome completeness and a streamlined genome structure. The information indicates the minimal genomic features required by both the endofungal lifestyle and artificial cultivation, which furthers our understanding of genome reduction in fungal endosymbionts and extends the culture resources for biotechnological development on engineering synthetic microbiomes.

A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze.

High-throughput SNP genotyping has become a precondition to move to higher precision and wider genome coverage genetic analysis of natural and breeding populations of non-model species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation, SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual genome-wide patterns of genetic diversity and structure, challenging previous microsatellite-based assessments. Moreover, SNPs corroborated the known major north-south genetic cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public, user-friendly 3K SNP array for A. angustifolia and a catalog of 44,318 SNPs predicted to provide ~29,000 informative SNPs across ~20,000 loci across the genome, will allow tackling still unsettled questions on its evolutionary history, toward a more comprehensive picture of the origin, past dynamics and future trend of the species' genetic resources. Additionally, but not less importantly, the SNP array described, unlocks the potential to adopt genomic prediction methods to accelerate the still very timid efforts of systematic tree breeding of A. angustifolia.

Characterization of a novel Pantoea symbiont allows inference of a pattern of convergent genome reduction in bacteria associated with Pentatomidae.

Phytophagous stink bugs typically harbor nutritional symbiotic bacteria in their midgut, to integrate their unbalanced diet. In the Pentatomidae, most symbionts are affiliated to the genus Pantoea, and are polyphyletic. This suggests a scenario of an ancestral establishment of symbiosis, followed by multiple symbiont replacement events by akin environmental bacteria in different host lineages. In this study, a novel Pantoeaspecies ('CandidatusPantoea persica') was characterized from the gut of the pentatomid Acrosternum arabicum, and shown to be highly abundant in a specific portion of the gut and necessary for the host development. The genome of the symbiont (2.9 Mb), while presenting putative host-supportive metabolic pathways, including those for amino acids and vitamin synthesis, showed a high level of pseudogenization, indicating ongoing genome reduction. Comparative analyses with other free-living and symbiotic Pantoea highlighted a convergent pattern of genome reduction in symbionts of pentatomids, putatively following the typical phases modelized in obligate nutritional symbionts of insects. Additionally, this system has distinctive traits, as hosts are closely related, and symbionts originated multiple independent times from closely related free-living bacteria, displaying convergent and independent conspicuous genome reduction. Due to such peculiarities, this may become an ideal model to study genome evolutionary processes in insect symbionts.

Morphological and genome-wide evidence for natural hybridisation within the genus Stipa (Poaceae)

Hybridisation in the wild between closely related species is a common mechanism of speciation in the plant kingdom and, in particular, in the grass family. Here we explore the potential for natural hybridisation in Stipa (one of the largest genera in Poaceae) between genetically distant species at their distribution edges in Mountains of Central Asia using integrative taxonomy. Our research highlights the applicability of classical morphological and genome reduction approaches in studies on wild plant species. The obtained results revealed a new nothospecies, Stipa × lazkovii, which exhibits intermediate characters to S. krylovii and S. bungeana. A high-density DArTseq assay disclosed that S. × lazkovii is an F1 hybrid, and established that the plastid and mitochondrial DNA was inherited from S. bungeana. In addition, molecular markers detected a hybridisation event between morphologically and genetically distant species S. bungeana and probably S. glareosa. Moreover, our findings demonstrated an uncertainty on the taxonomic status of S. bungeana that currently belongs to the section Leiostipa, but it is genetically closer to S. breviflora from the section Barbatae. Finally, we noticed a discrepancy between the current molecular data with the previous findings on S. capillata and S. sareptana.

Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes

The evolutionary processes that drive variation in genome size across the tree of life remain unresolved. Effective population size (Ne) is thought to play an important role in shaping genome size [1-3]-a key example being the reduced genomes of insect endosymbionts, which undergo population bottlenecks during transmission [4]. However, the existence of reduced genomes in marine and terrestrial prokaryote species with large Ne indicate that genome reduction is influenced by multiple processes [3]. One candidate process is enhanced mutation rate, which can increase adaptive capacity but can also promote gene loss. To investigate evolutionary forces associated with prokaryotic genome reduction, we performed molecular evolutionary and phylogenomic analyses of nine lineages from five bacterial and archaeal phyla. We found that gene-loss rate strongly correlated with synonymous substitution rate (a proxy for mutation rate) in seven of the nine lineages. However, gene-loss rate showed weak or no correlation with the ratio of nonsynonymous/synonymous substitution rate (dN/dS). These results indicate that genome reduction is largely associated with increased mutation rate, while the association between gene loss and changes in Ne is less well defined. Lineages with relatively high dS and dN, as well as smaller genomes, lacked multiple DNA repair genes, providing a proximate cause for increased mutation rates. Our findings suggest that similar mechanisms drive genome reduction in both intracellular and free-living prokaryotes, with implications for developing a comprehensive theory of prokaryote genome size evolution.

The origin and evolution of viruses inferred from fold family structure.

The canonical frameworks of viral evolution describe viruses as cellular predecessors, reduced forms of cells, or entities that escaped cellular control. The discovery of giant viruses has changed these standard paradigms. Their genetic, proteomic and structural complexities resemble those of cells, prompting a redefinition and reclassification of viruses. In a previous genome-wide analysis of the evolution of structural domains in proteomes, with domains defined at the fold superfamily level, we found the origins of viruses intertwined with those of ancient cells. Here, we extend these data-driven analyses to the study of fold families confirming the co-evolution of viruses and ancient cells and the genetic ability of viruses to foster molecular innovation. The results support our suggestion that viruses arose by genomic reduction from ancient cells and validate a co-evolutionary ‘symbiogenic’ model of viral origins.Electronic supplementary materialThe online version of this article (10.1007/s00705-020-04724-1) contains supplementary material, which is available to authorized users.

Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog

Currently described members of Elusimicrobia, a relatively recently defined phylum, are animal-associated and rely on fermentation. However, free-living Elusimicrobia have been detected in sediments, soils and groundwater, raising questions regarding their metabolic capacities and evolutionary relationship to animal-associated species. Here, we analyzed 94 draft-quality, non-redundant genomes, including 30 newly reconstructed genomes, from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 of which previously lacked reference genomes. Groundwater-associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles, reliant on oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds and Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis with hydrogen and carbon dioxide as the substrates. Genomes from two clades of groundwater-associated Elusimicrobia often encode a new group of nitrogenase paralogs that co-occur with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. We identified similar genomic loci in genomes of bacteria from the Gracilibacteria phylum and the Myxococcales order and predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associated Elusimicrobia clades nest phylogenetically within two free-living-associated clades. Thus, we propose an evolutionary trajectory in which some Elusimicrobia adapted to animal-associated lifestyles from free-living species via genome reduction.

Genomic and Transcriptomic Characterisation of Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer.

Standard treatment for locally advanced rectal cancer (LARC) is neoadjuvant chemoradiotherapy (NACRT), followed by surgical resection. However, >70% of patients do not achieve a complete pathological response and have higher rates of relapse and death. There are no validated pre- or on-treatment factors that predict response to NACRT besides tumour stage and size. We characterised the response of 33 LARC patients to NACRT, collected tumour samples from patients prior to, during and after NACRT, and performed whole exome, transcriptome and high-depth targeted sequencing. The pre-treatment LARC genome was not predictive of response to NACRT. However, in line with the increasing recognition of microbial influence in cancer, RNA analysis of pre-treatment tumours suggested a greater abundance of Fusobacteria in intermediate and poor responders. In addition, we investigated tumour heterogeneity and evolution in response to NACRT. While matched pre-treatment, on-treatment and post-treatment tumours revealed minimal genome evolution overall, we identified cases in which microsatellite instability developed or was selected for during NACRT. Recent research has suggested a role for adaptive mutability to targeted therapy in colorectal cancer cells. We provide preliminary evidence of selection for mismatch repair deficiency in response to NACRT. Furthermore, pre-NACRT genomic landscapes do not predict treatment response but pre-NACRT microbiome characteristics may be informative.

An emerging role for cyclic dinucleotide phosphodiesterase and nanoRNase activities in Mycoplasma bovis: Securing survival in cell culture.

Mycoplasmas are host-restricted prokaryotes with a nearly minimal genome. To overcome their metabolic limitations, these wall-less bacteria establish intimate interactions with epithelial cells at mucosal surfaces. The alarming rate of antimicrobial resistance among pathogenic species is of particular concern in the medical and veterinary fields. Taking advantage of the reduced mycoplasma genome, random transposon mutagenesis was combined with high-throughput screening in order to identify key determinants of mycoplasma survival in the host-cell environment and potential targets for drug development. With the use of the ruminant pathogen Mycoplasma bovis as a model, three phosphodiesterases of the DHH superfamily were identified as essential for the proliferation of this species under cell culture conditions, while dispensable for axenic growth. Despite a similar domain architecture, recombinant Mbov_0327 and Mbov_0328 products displayed different substrate specificities. While rMbovP328 protein exhibited activity towards cyclic dinucleotides and nanoRNAs, rMbovP327 protein was only able to degrade nanoRNAs. The Mbov_0276 product was identified as a member of the membrane-associated GdpP family of phosphodiesterases that was found to participate in cyclic dinucleotide and nanoRNA degradation, an activity which might therefore be redundant in the genome-reduced M. bovis. Remarkably, all these enzymes were able to convert their substrates into mononucleotides, and medium supplementation with nucleoside monophosphates or nucleosides fully restored the capacity of a Mbov_0328/0327 knock-out mutant to grow under cell culture conditions. Since mycoplasmas are unable to synthesize DNA/RNA precursors de novo, cyclic dinucleotide and nanoRNA degradation are likely contributing to the survival of M. bovis by securing the recycling of purines and pyrimidines. These results point toward proteins of the DHH superfamily as promising targets for the development of new antimicrobials against multidrug-resistant pathogenic mycoplasma species.

Dynamics of Insect-Microbiome Interaction Influence Host and Microbial Symbiont.

Insects share an intimate relationship with their gut microflora and this symbiotic association has developed into an essential evolutionary outcome intended for their survival through extreme environmental conditions. While it has been clearly established that insects, with very few exceptions, associate with several microbes during their life cycle, information regarding several aspects of these associations is yet to be fully unraveled. Acquisition of bacteria by insects marks the onset of microbial symbiosis, which is followed by the adaptation of these bacterial species to the gut environment for prolonged sustenance and successful transmission across generations. Although several insect–microbiome associations have been reported and each with their distinctive features, diversifications and specializations, it is still unclear as to what led to these diversifications. Recent studies have indicated the involvement of various evolutionary processes operating within an insect body that govern the transition of a free-living microbe to an obligate or facultative symbiont and eventually leading to the establishment and diversification of these symbiotic relationships. Data from various studies, summarized in this review, indicate that the symbiotic partners, i.e., the bacteria and the insect undergo several genetic, biochemical and physiological changes that have profound influence on their life cycle and biology. An interesting outcome of the insect-microbe interaction is the compliance of the microbial partner to its eventual genome reduction. Endosymbionts possess a smaller genome as compared to their free-living forms, and thus raising the question what is leading to reductive evolution in the microbial partner. This review attempts to highlight the fate of microbes within an insect body and its implications for both the bacteria and its insect host. While discussion on each specific association would be too voluminous and outside the scope of this review, we present an overview of some recent studies that contribute to a better understanding of the evolutionary trajectory and dynamics of the insect-microbe association and speculate that, in the future, a better understanding of the nature of this interaction could pave the path to a sustainable and environmentally safe way for controlling economically important pests of crop plants.