BACKGROUND: The repeats in toxin (Rtx) are an important pathogenicity factor involved in host cells invasion of Legionella pneumophila and other pathogenic bacteria. Its role in escaping the host immune system and cytotoxic activity is well known. Its repeated motives and modularity make Rtx a multifunctional factor in pathogenicity. RESULTS: The comparative analysis of rtx gene among 6 strains of L. pneumophila showed modularity in their structures. Among compared genomes, the N-terminal region of the protein presents highly dissimilar repeats with functionally similar domains. On the contrary, the C-terminal region is maintained with a fashionable modular configuration, which gives support to its proposed role in adhesion and pore formation. Despite the variability of rtx among the considered strains, the flanking genes are maintained in synteny and similarity. CONCLUSION: In contrast to the extracellular bacteria Vibrio cholerae, in which the rtx gene is highly conserved and flanking genes have lost synteny and similarity, the gene region coding for the Rtx toxin in the intracellular pathogen L. pneumophila shows a rapid evolution. Changes in the rtx could play a role in pathogenicity. The interplay of the Rtx toxin with host membranes might lead to the evolution of new variants that are able to escape host cell defences. ; This work has been funded by grant BMC2006-06003 from MEC to AL and by contract with Conselleria de Sanidad of Valencian Government to AM. Nuria Jiménez is recipient of a fellowship from Carlos III and Giuseppe D'Auria has a research contract from CIBERESP. Sequencing was carried out using facilities of the SCSIE from University of Valencia. ; Sí
Bacterial endosymbionts and their insect hosts establish an intimate metabolic relationship. Bacteria offer a variety of essential nutrients to their hosts, whereas insect cells provide the necessary sources of matter and energy to their tiny metabolic allies. These nutritional complementations sustain themselves on a diversity of metabolite exchanges between the cell host and the reduced yet highly specialized bacterial metabolism-which, for instance, overproduces a small set of essential amino acids and vitamins. A well-known case of metabolic complementation is provided by the cedar aphid Cinara cedri that harbors two co-primary endosymbionts, Buchnera aphidicola BCc and Ca. Serratia symbiotica SCc, and in which some metabolic pathways are partitioned between different partners. Here we present a genome-scale metabolic network (GEM) for the bacterial consortium from the cedar aphid iBSCc. The analysis of this GEM allows us the confirmation of cases of metabolic complementation previously described by genome analysis (i.e., tryptophan and biotin biosynthesis) and the redefinition of an event of metabolic pathway sharing between the two endosymbionts, namely the biosynthesis of tetrahydrofolate. In silico knock-out experiments with iBSCc showed that the consortium metabolism is a highly integrated yet fragile network. We also have explored the evolutionary pathways leading to the emergence of metabolic complementation between reduced metabolisms starting from individual, complete networks. Our results suggest that, during the establishment of metabolic complementation in endosymbionts, adaptive evolution is significant in the case of tryptophan biosynthesis, whereas vitamin production pathways seem to adopt suboptimal solutions. ; We would like to thank the Obra Social Programme of La Caixa Savings Bank for the doctoral fellowship granted to JC-E. Financial support from Spanish Government (grant reference: BFU2015-64322-C2-1-R co-financed by FEDER funds and Ministerio de Economía y Competitividad) and Generalitat Valenciana (grant reference: PROMETEOII/2014/065) is gratefully acknowledged. MM acknowledges financial support from Sapienza, University of Rome. DT acknowledges support by a European Union grant from the Marie Curie ITN SYMBIOMICS (264774) and a grant from the Knut and Alice Wallenberg Foundation (2012.0075), given to Björn Andersson (Karolinska Institute) and Siv Andersson (Uppsala University). ; Peer reviewed
An increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that had developed CRC and had undergone surgical resection. Formalin-fixed paraffin embedded (FFPE) tissue blocks from matched colorectal and normal mucosa were used for genomic DNA extraction with a commercial kit and sequenced by high-throughput sequencing. A metagenomic approach enabled the taxonomic and functional identification of the microbial community and associated genes detected in the specimens. Slightly lower taxonomic diversity was observed in the tumor compared to the non-tumor tissue. Furthermore, the most remarkable differences between tumors and healthy tissue was the significant increase in the genus Fusobacterium in the former, in particular the species F. nucleatum, as well as Camplylobacter or Bacteroides fragilis, in accordance with previous studies of CRC. However, unlike prior studies, the present work is not based on directed detection by qPCR but instead uses a metagenomic approach to retrieve the whole bacterial community, and addresses the additional difficulty of using long-term stored FFPE samples. ; We want to particularly acknowledge the patients and the Biobank IBSP-CV (PT17/0015/0017) integrated in the Spanish National Biobanks Network and in the Valencian Biobanking Network, especially A. Ahicart, D. Molina and J. Martínez, for their collaboration. This research was funded by grants to AM from the Fundación Científica de la Asociación Española contra el Cancer (project AECC 2017-1485), including a post-doctoral contract to VPB first and to SRR later. GD is recipient of a PhD fellowship from the Junta Asociada Provincial de Valencia AECC. Action co-financed by the European Union through the Operational Program of European Regional Development Fund (ERDF) of Valencia Region (Spain) 2014-2020. ; Peer reviewed
An increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that had developed CRC and had undergone surgical resection. Formalin-fixed paraffin embedded (FFPE) tissue blocks from matched colorectal and normal mucosa were used for genomic DNA extraction with a commercial kit and sequenced by high-throughput sequencing. A metagenomic approach enabled the taxonomic and functional identification of the microbial community and associated genes detected in the specimens. Slightly lower taxonomic diversity was observed in the tumor compared to the non-tumor tissue. Furthermore, the most remarkable differences between tumors and healthy tissue was the significant increase in the genus Fusobacterium in the former, in particular the species F. nucleatum, as well as Camplylobacter or Bacteroides fragilis, in accordance with previous studies of CRC. However, unlike prior studies, the present work is not based on directed detection by qPCR but instead uses a metagenomic approach to retrieve the whole bacterial community, and addresses the additional difficulty of using long-term stored FFPE samples. ; This research was funded by grants to AM from the Fundación Científica de la Asociación Española contra el Cancer (project AECC 2017-1485), including a post-doctoral contract to VPB first and to SRR later. GD is recipient of a PhD fellowship from the Junta Asociada Provincial de Valencia AECC. Action co-financed by the European Union through the Operational Program of European Regional Development Fund (ERDF) of Valencia Region (Spain) 2014-2020.
In this article, we introduce ARES (Antibiotic Resistance Evolution Simulator) a software device that simulates P-system model scenarios with five types of nested computing membranes oriented to emulate a hierarchy of eco-biological compartments, i.e. a) peripheral ecosystem; b) local environment; c) reservoir of supplies; d) animal host; and e) host's associated bacterial organisms (microbiome). Computational objects emulating molecular entities such as plasmids, antibiotic resistance genes, antimicrobials, and/or other substances can be introduced into this framework and may interact and evolve together with the membranes, according to a set of pre-established rules and specifications. ARES has been implemented as an online server and offers additional tools for storage and model editing and downstream analysis ; This work has also been supported by grants BFU2012-39816-C02-01 (co-financed by FEDER funds and the Ministry of Economy and Competitiveness, Spain) to AL and Prometeo/2009/092 (Ministry of Education, Government of Valencia, Spain) and Explora Ciencia y Explora Tecnologia/SAF2013-49788-EXP (Spanish Ministry of Economy and Competitiveness) to AM. IRF is recipient of a "Sara Borrell" postdoctoral fellowship (Ref. CD12/00492) from the Ministry of Economy and Competitiveness (Spain). We are also grateful to the Spanish Network for the Study of Plasmids and Extrachromosomal Elements (REDEEX) for encouraging and funding cooperation among Spanish microbiologists working on the biology of mobile genetic elements (Spanish Ministry of Science and Innovation, reference number BFU2011-14145-E). ; Campos Frances, M.; Llorens, C.; Sempere Luna, JM.; Futami, R.; Rodríguez, I.; Carrasco, P.; Capilla, R. (2015). A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES). Biology Direct. 10(41):1-13. https://doi.org/10.1186/s13062-015-0070-9 ; S ; 1 ; 13 ; 10 ; 41 ; Baquero F, Coque TM, Canton R. Counteracting antibiotic resistance: breaking ...
cis-Encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of most of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. We show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asRNAs is exponentially dependent on the genomic AT content and that expression of asRNA at low levels exerts little impact in terms of energy consumption. A transcription model simulating mRNA and asRNA production indicates that the asRNA regulatory effect is only observed above certain expression thresholds, substantially higher than physiological transcript levels. These predictions were verified experimentally by overexpressing nine different asRNAs in Mycoplasma pneumoniae. Our results suggest that most of the antisense transcripts found in bacteria are the consequence of transcriptional noise, arising at spurious promoters throughout the genome. ; This work was supported by the European Union Seventh Framework Programme (FP7/2007–2013), through the European Research Council (232913); Fundación Botín, the Spanish Ministry of Economy and Competitiveness (BIO2007-61762); National Plan of R + D + i; ISCIII—Subdirección General de Evaluación y Fomento de la Investigación (PI10/01702); European Regional Development Fund (to the Institució Catalana de Recerca i Estudis Avançats research professor L.S.); and Spanish Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa 2013–2017" (SEV-2012-0208). A.L. received grant BFU2012-39816-C02-01 from the Spanish Ministry of Economy and Competitivity cofinanced by FEDER (Fondo Europeo de Desarrollo Regional) funds.
Large-scale gene duplication, including whole-genome duplication (WGD), is a very common phenomenon in eukaryotic genomes. Bursts of gene duplications are considered a major source of evolutionary innovation and have been associated with the increase in biological complexity and adaptive radiations of species (Zhang 2003). In particular, large-scale gene duplications, generally associated with WGDs, have been reported for many eukaryotic lineages including plants (Van de Peer et al. 2017), fungi (Marcet-Houben and Gabaldón 2015), and animals (Taylor et al. 2001). Although large-scale duplication seems less pervasive in animals than in plants, a growing number of studies report such events in animals. Among other lineages, putative WGDs have been described at the base of vertebrates (Ohno 1970; Dehal and Boore 2005; Putnam et al. 2008), and in several lineages of fish (Christoffels et al. 2004; Glasauer and Neuhauss 2014), amphibians (Mable et al. 2011; Session et al. 2016), and arthropods (Jacobson et al. 2013; Kenny et al. 2016; Schwager et al. 2017; Li et al. 2018). Aphids belong to the infraorder Aphidomorpha that includes three families: Aphididae, Adelgidae, and Phylloxeridae (Favret 2013; Nováková et al. 2013; Blackman and Eastop 2000). Aphids and related (Aphidomorpha) species (Becker-Migdisova and Aizenberg 1962) are hemipteran insects that feed on plant sap (Tjallingii 1995). This specialized diet, rich in carbohydrates but poor in nitrogen compounds, has resulted in several adaptations including the establishment of tight relationships with bacterial endosymbionts (Scarborough et al. 2005; Moya et al. 2008; von Dohlen et al. 2017). There are more than 5,000 described aphid species, of which, about 450 have been collected from crop plants, and 100 are considered of significant economic importance (Van Emden and Harrington 2017). Genomes of several aphid species of agricultural interest have been sequenced, including Acyrthosiphon pisum, Myzus persicae, Diuraphis noxia, Aphis glycines, and Sipha flava (International Aphid Genomics Consortium 2010; Nicholson et al. 2015; Mathers et al. 2017; Wenger et al. 2017). However, except for S. flava (subfamily Chaitophorinae), the sequenced aphids belong to a single subfamily, Aphidinae, limiting our understanding of the genomic diversity in this group of insects. Remarkably, most genome analyses in these species have revealed an important number of paralogous sequences and expanded gene families, including amino acid transporters, odorant and gustatory receptor genes, miRNA-specific dicer-1, ago1 genes, and pasha, among others (Smadja et al. 2009; Huerta-Cepas et al. 2010; Jaubert-Possamai et al. 2010; Duncan et al. 2016; Mathers et al. 2017). However, the close relatedness of the sequenced species provides little resolution to the phylogenetic placement of the duplication events, particularly the ancestral ones. Recent studies have focused on assessing patterns of sequence and expression divergence among recently duplicated genes in A. pisum (Fernández et al. 2019) or M. persicae (Mathers et al. 2017). They have also inspected the distribution of old and young A. pisum paralogs along chromosomes, by categorizing the age of genes that are best-reciprocal hits of each other based on the amount of synonymous substitutions (Li et al. 2019). However, we still lack a proper understanding of when the ancestral duplications occurred, and whether they can be linked to phenotypic innovations shared by aphids or related species. To better assess the origin of the paralogous genes of aphids we sequenced the genome of Cinara cedri (Lachninae subfamily, tribe Eulachnini), the first representative genome from an early-branching lineage of the Aphididae family. Cinara species (and most Lachninae) are particular among aphids as they feed on conifers (gymnosperms), whereas all the other genome-sequenced aphids feed on angiosperms. Another clear difference between the Lachninae and the rest of aphids is that two co-obligate endosymbionts (Buchnera aphidicola, Serratia symbiotica) are present in this group, whereas only B. aphidicola is obligate for the rest of aphids (Latorre and Manzano-Marín 2017). We used a phylogeny-based approach (Huerta-Cepas and Gabaldón 2011) to provide the relative timing of aphid duplications in a phylogenetic framework that includes 21 other fully sequenced genomes and two transcriptomes. Our results provide compelling evidence for an ancestral wave of gene duplications, whose origin predates the diversification of all sequenced aphids, adelgids, and phyloxerids, but are subsequent to their divergence from the Coccoidea lineage, ∼106–227 Ma. ; This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF). The authors want to thank Sophia Derdak for her help in the genome polishing step. ; Peer Reviewed ; Postprint (published version)
Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106–227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings. ; This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF). ; Peer reviewed
Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106-227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings. ; This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF). The genome, annotation and sequencing reads have been deposited at the European Nucleotide Archive (ENA) under the project accession PRJEB33415
