0000000000188869
AUTHOR
Rosario Gil
The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii
Background Bacterial symbioses are widespread among insects. The early establishment of such symbiotic associations has probably been one of the key factors for the evolutionary success of insects, since it may have allowed access to novel ecological niches and to new imbalanced food resources, such as plant sap or blood. Several genomes of bacterial endosymbionts of different insect species have been recently sequenced, and their biology has been extensively studied. Recently, the complete genome sequence of Candidatus Carsonella ruddii, considered the primary endosymbiont of the psyllid Pachpsylla venusta, has been published. This genome consists of a circular chromosome of 159,662 bp and…
Bacterial antisense RNAs are mainly the product of transcriptional noise
Most of the antisense transcripts in bacteria are the product of transcriptional noise derived from spurious promoters.
Natural Occurrence of Secondary Bacterial Symbionts in Aphids from Tunisia, with a Focus on Genus Hyalopterus
Aphids (Hemiptera: Aphididae) can harbor two types of bacterial symbionts. In addition to the obligate endosymbiont Buchnera aphidicola Munson, Baumann and Kinsey 1991 (Enterobacteriales: Enterobacteriaceae), several facultative symbiotic bacteria, called secondary (S) symbionts, have been identified among many important pest aphid species. To determine interpopulational diversity of S-symbionts, we carried out a survey in a total of 18 populations of six aphid species collected from six localities in Tunisia, by performing a diagnostic polymerase chain reaction analysis of partial 16S-23S rRNA operon sequences. While 61.7% of individuals contained only Buchnera, three S-symbionts were foun…
Cytogenetics, flow cytometry, cytophotometry and morphometry of 22 cases of primary breast carcinoma. A comparative study.
Cytogenetic, flow cytometric, cytophotometric and morphometric analyses were performed on 22 previously untreated, primary solid breast carcinomas. Although the cell nuclei as the primary object of these studies were the same in all the tumors, distinct features were evaluated in each case to determine to what degree the results obtained by these techniques are comparable. From the cytogenetic viewpoint, six tumors had a modal number in the diploid range, seven were in the triploid range, and two in the tetraploid range; seven tumors had no modal number. These data correlate with the flow cytometry and cytophotometry results obtained, with DNA values slightly higher than their respective ch…
Comparative analysis of two genomic regions among four strains of Buchnera aphidicola, primary endosymbiont of aphids
Preliminary analysis of two selected genomic regions of Buchnera aphidicola BCc, the primary endosymbiont of the cedar aphid Cinara cedri, has revealed a number of interesting features when compared with the corresponding homologous regions of the three B. aphidicola genomes previously sequenced, that are associated with different aphid species. Both regions exhibit a significant reduction in length and gene number in B. aphidicola BCc, as it could be expected since it possess the smallest bacterial genome. However, the observed genome reduction is not even in both regions, as it appears to be dependent on the nature of their gene content. The region fpr-trxA, that contains mainly metabolic…
An unusual translocation associated with recurrent spontaneous abortions
The authors report a case of 11;17 translocation associated with recurrent spontaneous abortions, and request contact with colleagues who have observed similar cases.
Interkingdom Gut Microbiome and Resistome of the Cockroach Blattella germanica
Cockroaches are intriguing animals with two coexisting symbiotic systems, an endosymbiont in the fat body, involved in nitrogen metabolism, and a gut microbiome whose diversity, complexity, role, and developmental dynamics have not been fully elucidated. In this work, we present a metagenomic approach to study Blattella germanica populations not treated, treated with kanamycin, and recovered after treatment, both naturally and by adding feces to the diet, with the aim of better understanding the structure and function of its gut microbiome along the development as well as the characterization of its resistome.
Patterns and rates of nucleotide substitution, insertion and deletion in the endosymbiont of antsBlochmannia floridanus
Genome reduction is a general process that has been studied in numerous symbiotic bacteria associated with insects. We investigated the last stages of genome degradation in Blochmannia floridanus, a mutualistic bacterial endosymbiont of the ant Camponotus floridanus. We determined the tempo (rates of insertion and deletion) and mode (size and number of insertion-deletion events) of the process in the last 200,000 years by analysing a total of 16 intergenic regions in several strains of this endosymbiont from different ant populations. We provide the first calculation of the reduction rate for noncoding DNA in this endosymbiont (2.2 x 10(-8) lost nucleotides/site/year) and compare it with th…
Structural analyses of a hypothetical minimal metabolism
By integrating data from comparative genomics and large-scale deletion studies, we previously proposed a minimal gene set comprising 206 protein-coding genes. To evaluate the consistency of the metabolism encoded by such a minimal genome, we have carried out a series of computational analyses. Firstly, the topology of the minimal metabolism was compared with that of the reconstructed networks from natural bacterial genomes. Secondly, the robustness of the metabolic network was evaluated by simulated mutagenesis and, finally, the stoichiometric consistency was assessed by automatically deriving the steady-state solutions from the reaction set. The results indicated that the proposed minimal …
Congenital hyperthyroidism with reciprocal translocation t(1;17)(q25;q21)
The authors report a case of 1;17 translocation and request contact with colleagues who have observed similar cases.
The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes
Bacterial symbioses are widespread among insects, probably being one of the key factors of their evolutionary success. We present the complete genome sequence of Blochmannia floridanus , the primary endosymbiont of carpenter ants. Although these ants feed on a complex diet, this symbiosis very likely has a nutritional basis: Blochmannia is able to supply nitrogen and sulfur compounds to the host while it takes advantage of the host metabolic machinery. Remarkably, these bacteria lack all known genes involved in replication initiation ( dna A, pri A, and rec A). The phylogenetic analysis of a set of conserved protein-coding genes shows that Bl. floridanus is phylogenetically related to Buch…
Complete Genome Sequence of “Candidatus Tremblaya princeps” Strain PCVAL, an Intriguing Translational Machine below the Living-Cell Status
ABSTRACT The sequence of the genome of “ Candidatus Tremblaya princeps” strain PCVAL, the primary endosymbiont of the citrus mealybug Planococcus citri , has been determined. “ Ca . Tremblaya princeps” presents an unusual nested endosymbiosis and harbors a gammaproteobacterial symbiont within its cytoplasm in all analyzed mealybugs. The genome sequence reveals that “ Ca . Tremblaya princeps” cannot be considered an independent organism but that the consortium with its gammaproteobacterial symbiotic associate represents a new composite living being.
Seasonal Changes in the Endosymbiotic Consortia of Aphids from the Genus <i>Cinara</i>
Buchnera aphidicola is the primary endosymbiont of aphids with which it maintains an obligate mutualistic symbiotic relationship. Insects also maintain facultative symbiotic relationships with secondary symbionts, and Serratia symbiotica is the most common in aphids. The presence of both symbionts in aphids of the subfamily Lachninae has been widely studied by our group. We examined two closely related aphids, Cinara tujafilina and C. cedri in the present study. Even though both B. aphidicola strains have similar genome sizes and gene contents, the genomes of the two S. symbiotica strains were markedly different. The SCc strain has the smallest genome known for this species, while SCt posse…
Gut Microbiota Cannot Compensate the Impact of (quasi) Aposymbiosis in Blattella germanica
Simple Summary The German cockroach Blattella germanica is a good model to study complex symbiotic relationships because the following two symbiotic systems coexist in a single individual: the endosymbiont Blattabacterium (living inside specialized cells called bacteriocytes) and the gut microbiota. Although the role of the endosymbiont has been fully elucidated, the function of the gut microbiota remains unclear. The study of the gut microbiota will benefit from the availability of insects deprived of Blattabacterium. Our goal is to determine the effect of the removal (or, at least, the reduction) of the endosymbiont population on the cockroach’s fitness, in a normal gut microbiota communi…
A novel cell wall protein specific to the mycelial form of Yarrowia lipolytica.
A cDNA clone specifying a cell wall protein was isolated from a Yarrowia lipolytica cDNA library. The cDNA library was constructed in the expression vector lambda gt 11, with the RNA isolated from actively growing mycelial cells. The deduced amino acid sequence shows that the encoded protein contains an N-terminal hydrophobic signal peptide. We have designated this protein YWP1 for Yarrowia lipolytica cell Wall Protein. Northern hybridization identified YWP1 transcript only when Y. lipolytica was growing in the mycelial form. The encoded protein seems to be covalently bound to the glucan cell wall since it is not released from the cell walls by sodium dodecyl sulphate extraction, but it is …
Et tu, Brute? Not Even Intracellular Mutualistic Symbionts Escape Horizontal Gene Transfer
Many insect species maintain mutualistic relationships with endosymbiotic bacteria. In contrast to their free-living relatives, horizontal gene transfer (HGT) has traditionally been considered rare in long-term endosymbionts. Nevertheless, meta-omics exploration of certain symbiotic models has unveiled an increasing number of bacteria-bacteria and bacteria-host genetic transfers. The abundance and function of transferred loci suggest that HGT might play a major role in the evolution of the corresponding consortia, enhancing their adaptive value or buffering detrimental effects derived from the reductive evolution of endosymbionts' genomes. Here, we comprehensively review the HGT cases recor…
A novel intracellular mutualistic bacterium in the invasive ant Cardiocondyla obscurior.
The evolution of eukaryotic organisms is often strongly influenced by microbial symbionts that confer novel traits to their hosts. Here we describe the intracellular Enterobacteriaceae symbiont of the invasive ant Cardiocondyla obscurior, 'Candidatus Westeberhardia cardiocondylae'. Upon metamorphosis, Westeberhardia is found in gut-associated bacteriomes that deteriorate following eclosion. Only queens maintain Westeberhardia in the ovarian nurse cells from where the symbionts are transmitted to late-stage oocytes during nurse cell depletion. Functional analyses of the streamlined genome of Westeberhardia (533 kb, 23.41% GC content) indicate that neither vitamins nor essential amino acids a…
How Does Tremblaya princeps Get Essential Proteins from Its Nested Partner Moranella endobia in the Mealybug Planoccocus citri?
International audience; Many insects maintain intracellular mutualistic symbiosis with a wide range of bacteria which are considered essential for their survival (primary or P-endosymbiont) and typically suffer drastic genome degradation. Progressive loss of P-endosymbiont metabolic capabilities could lead to the recruitment of co-existent facultative endosymbiont (secondary or S-endosymbiont), thus adding more complexity to the symbiotic system. Planococcus citri, among other mealybug species, harbors an unconventional nested endosymbiotic system where every Tremblaya princeps cell (beta-proteobacterium) harbors many Moranella endobia cells (gamma-proteobacterium). In this system, T. princ…
Factors Behind Junk DNA in Bacteria
Although bacterial genomes have been traditionally viewed as being very compact, with relatively low amounts of repetitive and non-coding DNA, this view has dramatically changed in recent years. The increase of available complete bacterial genomes has revealed that many species present abundant repetitive DNA (i.e., insertion sequences, prophages or paralogous genes) and that many of these sequences are not functional but can have evolutionary consequences as concerns the adaptation to specialized host-related ecological niches. Comparative genomics analyses with close relatives that live in non-specialized environments reveal the nature and fate of this bacterial junk DNA. In addition, the…
An azoospermic male with reciprocal translocation t(1;15)(q11;p11)
The authors report on a case of 1;15 translocation and request contact with any colleagues who have observed similar cases.
Isolation and characterization of Saccharomyces cerevisiae mutants resistant to aculeacin A
Aculeacin A is a lipopeptide that inhibits beta-glucan synthesis in yeasts. A number of Saccharomyces cerevisiae mutants resistant to this antibiotic were isolated, and four loci (ACR1, ACR2, ACR3, and ACR4) whose products are involved in the sensitivity to aculeacin A of yeast cells were defined. Mutants containing mutations in the four loci were also resistant to echinocandin B, another member of this lipopeptide family of antibiotics. In contrast, acr1, acr3, and acr4 mutants were resistant to papulacandin B (an antibiotic containing a disaccharide linked to two fatty acid chains that also inhibits beta-glucan synthesis), but acr2 mutants were susceptible to this antibiotic. This result …
The evolutionary history of symbiotic associations among bacteria and their animal hosts: a model
AbstractA model to explain the evolutionary history of animal-bacteria obligatory mutualistic symbiosis is presented. Dispensability of genes and genetic isolation are key factors in the reduction process of these bacterial genomes. Major steps in such genome reductive evolution, leading towards primary endoslmblosis, and the possibility of complementation or replacement by a secondary symbiont are also indicated. Yet, we need to understand what happens at the beginning of the adaptative process towards an obligate mutualistic relationship. For this purpose, we propose to sequence the complete genome of SOPE, the primary endosymbiont of the rice weevil.
Evolution of Prokaryote-Animal Symbiosis from a Genomics Perspective
Symbioses involving prokaryotes living in close relationship with eukaryotic cells have been widely studied from a genomic perspective, especially in the case of insects. In the process toward host accommodation, symbionts experience major genetic and phenotypic changes that can be detected in comparison with free-living relatives. But, as expected, several scenarios allowed the evolution of symbiotic associations, from the first stages of free-living bacteria, through secondary and facultative symbiosis, towards the final point of obligate primary endosymbiosis. Particular relevance has the association formed by the coexistence of several symbionts into a given host. A summary of findings …
Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life
Buchnera is a mutualistic intracellular symbiont of aphids. Their association began about 200 million years ago, with host and symbiont lineages evolving in parallel since that time. During this coevolutionary process, Buchnera has experienced a dramatic decrease of genome size, retaining only essential genes for its specialized lifestyle. Previous studies reported that genome size in Buchnera spp. is very uniform, suggesting that genome shrinkage occurred early in evolution, and that modern lineages retain the genome size of a common ancestor. Our physical mapping of Buchnera genomes obtained from five aphid lineages shows that the genome size is not conserved among them, but has been red…
Mealybugs nested endosymbiosis: going into the 'matryoshka' system in Planococcus citri in depth.
Abstract Background In all branches of life there are plenty of symbiotic associations. Insects are particularly well suited to establishing intracellular symbiosis with bacteria, providing them with metabolic capabilities they lack. Essential primary endosymbionts can coexist with facultative secondary symbionts which can, eventually, establish metabolic complementation with the primary endosymbiont, becoming a co-primary. Usually, both endosymbionts maintain their cellular identity. An exception is the endosymbiosis found in mealybugs of the subfamily Pseudoccinae, such as Planococcus citri, with Moranella endobia located inside Tremblaya princeps. Results We report the genome sequencing …
Morphometric and cytophotometric nuclear analysis of altered hepatocyte foci induced by N-nitrosomorpholine (NNM) and aflatoxin B1 (AFB1) in liver of Wistar rats
The progressive morphological changes in the liver during neoplastic transformation have been studied by histological, cytophotometric and morphometric methods in male Wistar rats treated with two carcinogens: N-nitrosomorpholine (NNM) and aflatoxin B1 (AFB1). Cytophotometric and morphometric analysis of hepatocyte nuclei using Feulgen-stained tissue sections were performed in morphologically normal hepatic parenchyma and in early preneoplastic foci composed of altered hepatocytes. Foci of clear cells, mixed cells and large basophilic cells possessed a ploidy distribution similar to the surrounding non-transformed parenchyma, while the small hyperbasophilic cell foci were predominantly dipl…
Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story
Buchnera aphidicola, the primary endosymbiont of aphids, has undergone important genomic and biochemical changes as an adaptation to intracellular life. The most important structural changes include a drastic genome reduction and the amplification of genes encoding key enzymes for the biosynthesis of amino acids by their translocation to plasmids. Molecular characterization through different aphid subfamilies has revealed that the genes involved in leucine and tryptophan biosynthesis show a variable fate, since they can be located on plasmids or on the chromosome in different lineages. This versatility contrasts with the genomic stasis found in three distantly related B. aphidicola strains …
Reciprocal translocation t(1;18)(p32;q21) in a patient with some phenotypical anomalies
The authors report on a case of 1;18 translocation and request contact with any colleagues who have observed similar cases.
RCS1, a gene involved in controlling cell size inSaccharomyces cerevisiae
Cloning and sequencing of RCS1, Saccharomyces cerevisiae gene whose product seems to be involved in timing the budding event of the cell cycle, is described. A haploid strain in which the 3'-terminal region of the chromosomal copy of the gene has been disrupted produces cells that are, on average, twice the size of cells of the parental strain. The critical size for budding in the mutant is similarly increased, and the disruption mutation is dominant in a diploid heterozygous for the RCS1 gene. Spores from this diploid have a reduced ability to germinate, the effect being more pronounced in the spores carrying the disrupted copy of RCS1. However, disrupted cells recover from alpha-factor tr…
Chromosomal stasis versus plasmid plasticity in aphid endosymbiont Buchnera aphidicola.
The study of three genomes of the aphid endosymbiont Buchnera aphidicola has revealed an extraordinary stasis: conservation of gene order and genetic composition of the chromosome, while the chromosome size and number of genes has reduced. The reduction in genome size appears to be ongoing since some lineages we now know to have even smaller chromosomes than the first B. aphidicola analysed. The current sequencing by our group of one of these smaller genomes with an estimated size of 450 kb, and its comparison with the other three available genomes provide insights into the nature of processes involved in shrinkage. We discuss whether B. aphidicola might be driven to extinction and be repla…
The Minimal Gene-Set Machinery
All known living beings are made of cells, each one of which stores in its genome all of the information required for its correct functioning. The advent of high-throughput sequencing technologies and improvements in bioinformatics tools have allowed the complete sequencing, functional analysis and comparison of thousands of genomes from different species, helping research groups to delineate the minimal set of functions necessary to keep a cell alive under defined environmental conditions. This knowledge can not only be used to obtain a better understanding of the phenomenon of life, but also has many direct biotechnological and biomedical implications. Keywords: minimal genome; orthologou…
Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage
Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described. In a previous study, we detected a trpB gene of gammaproteobacterial origin in 'Ca. Tremblaya phenacola' from two Phenacoccus species, apparently indicating an unusual case of horizonta…
Learning how to live together: genomic insights into prokaryote–animal symbioses
Our understanding of prokaryote-eukaryote symbioses as a source of evolutionary innovation has been rapidly increased by the advent of genomics, which has made possible the biological study of uncultivable endosymbionts. Genomics is allowing the dissection of the evolutionary process that starts with host invasion then progresses from facultative to obligate symbiosis and ends with replacement by, or coexistence with, new symbionts. Moreover, genomics has provided important clues on the mechanisms driving the genome-reduction process, the functions that are retained by the endosymbionts, the role of the host, and the factors that might determine whether the association will become parasitic…
Toward minimal bacterial cells: evolution vs. design.
Abstract Recent technical and conceptual advances in the biological sciences opened the possibility of the construction of newly designed cells. In this paper we review the state of the art of cell engineering in the context of genome research, paying particular attention to what we can learn on naturally reduced genomes from either symbiotic or free living bacteria. Different minimal hypothetically viable cells can be defined on the basis of several computational and experimental approaches. Projects aiming at simplifying living cells converge with efforts to make synthetic genomes for minimal cells. The panorama of this particular view of synthetic biology lead us to consider the use of d…
Of Cockroaches and Symbionts: Recent Advances in the Characterization of the Relationship between Blattella germanica and Its Dual Symbiotic System
This article belongs to the Collection Feature Review Papers for Life.
The Metabolic Building Blocks of a Minimal Cell
This article belongs to the Section Evolutionary Biology.
Genome degeneration and adaptation in a nascent stage of symbiosis
Symbiotic associations between animals and microbes are ubiquitous in nature, with an estimated 15% of all insect species harboring intracellular bacterial symbionts. Most bacterial symbionts share many genomic features including small genomes, nucleotide composition bias, high coding density, and a paucity of mobile DNA, consistent with long-term host association. In this study, we focus on the early stages of genome degeneration in a recently derived insect-bacterial mutualistic intracellular association. We present the complete genome sequence and annotation of Sitophilus oryzae primary endosymbiont (SOPE). We also present the finished genome sequence and annotation of strain HS, a close…
Determination of the Core of a Minimal Bacterial Gene Set
SUMMARY The availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. Trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. Six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. The available data from several systematic experimental approaches to define all the essential genes in some completely sequenced bacterial genomes were also considered, and a reconstruction of a minima…
Unity Makes Strength: A Review on Mutualistic Symbiosis in Representative Insect Clades
Settled on the foundations laid by zoologists and embryologists more than a century ago, the study of symbiosis between prokaryotes and eukaryotes is an expanding field. In this review, we present several models of insect–bacteria symbioses that allow for the detangling of most known features of this distinctive way of living, using a combination of very diverse screening approaches, including molecular, microscopic, and genomic techniques. With the increasing the amount of endosymbiotic bacteria genomes available, it has been possible to develop evolutionary models explaining the changes undergone by these bacteria in their adaptation to the intracellular host environment. The establishmen…
New Insights on the Evolutionary History of Aphids and Their Primary Endosymbiont Buchnera aphidicola
Since the establishment of the symbiosis between the ancestor of modern aphids and their primary endosymbiont,Buchnera aphidicola, insects and bacteria have coevolved. Due to this parallel evolution, the analysis of bacterial genomic features constitutes a useful tool to understand their evolutionary history. Here we report, based on data fromB. aphidicola, the molecular evolutionary analysis, the phylogenetic relationships among lineages and a comparison of sequence evolutionary rates of symbionts of four aphid species from three subfamilies. Our results support previous hypotheses of divergence ofB. aphidicolaand their host lineages during the early Cretaceous and indicate a closer relati…
Bacterial endosymbionts of insects: insights from comparative genomics.
The development of molecular techniques for the study of uncultured bacteria allowed the extensive study of the widespread association between insects and intracellular symbiotic bacteria. Most of the bacterial endosymbionts involved in such associations are gamma-proteobacteria, closely related to Escherichia coli. In recent years, five genomes from insect endosymbionts have been sequenced, allowing the performance of extensive genome comparative analysis that, as a complement of phylogenetic studies, and analysis on individual genes, can help to understand the different traits of this particular association, including how the symbiotic process is established, the explanation of the specia…