scholarly journals Idiosyncratic genome degradation in a bacterial endosymbiont of periodical cicadas

2017 ◽  
Author(s):  
Matthew A. Campbell ◽  
Piotr Łukasik ◽  
Chris Simon ◽  
John P. McCutcheon
Keyword(s):  
Size Structure ◽  
Large Fraction ◽  
Closely Related Species ◽  
Individual Gene ◽  
Bacterial Endosymbiont ◽  
Living Bacterium ◽  
The Common ◽  
Coding Capacity ◽  
Free Living Bacterium ◽  
Genome Degradation

SummaryWhen a free-living bacterium transitions to a host-beneficial endosymbiotic lifestyle, it almost invariably loses a large fraction of its genome [1, 2]. The resulting small genomes often become unusually stable in size, structure, and coding capacity [3-5]. Candidatus Hodgkinia cicadicola (Hodgkinia), a bacterial endosymbiont of cicadas, sometimes exemplifies this genomic stability. The Hodgkinia genome has remained completely co-linear in some cicadas diverged by tens of millions of years [6, 7]. But in the long-lived periodical cicada Magicicada tredecim, the Hodgkinia genome has split into dozens of tiny, gene-sparse genomic circles that sometimes reside in distinct Hodgkinia cells [8]. Previous data suggested that other Magicicada species harbor similarly complex Hodgkinia populations, but the timing, number of origins, and outcomes of the splitting process were unknown. Here, by sequencing Hodgkinia metagenomes from the remaining six Magicicada species and two sister species, we show that all Magicicada species harbor Hodgkinia populations of at least twenty genomic circles each. We find little synteny among the 256 Hodgkinia circles analyzed except between the most closely related species. Individual gene phylogenies show that Hodgkinia first split in the common ancestor of Magicicada and its closest known relatives, but that most splitting has occurred within Magicicada and has given rise to highly variable Hodgkinia gene dosages between cicada species. These data show that Hodgkinia genome degradation has proceeded down different paths in different Magicicada species, and support a model of genomic degradation that is stochastic in outcome and likely nonadaptive for the host. These patterns mirror the genomic instability seen in some mitochondria.

scholarly journals Isolation of a New Free-living Bacterium Containing R-bodies

Microbiology ◽  
1986 ◽  
Vol 132 (10) ◽  
pp. 2801-2805 ◽  
Author(s):  
M. C. FUSTE ◽  
M. D. SIMON-PUJOL ◽  
A. M. MARQUES ◽  
J. GUINEA ◽  
F. CONGREGADO
Keyword(s):  
Free Living ◽  
Living Bacterium ◽  
Free Living Bacterium

scholarly journals Idiosyncratic Genome Degradation in a Bacterial Endosymbiont of Periodical Cicadas

2017 ◽  
Vol 27 (22) ◽  
pp. 3568-3575.e3 ◽  
Author(s):  
Matthew A. Campbell ◽  
Piotr Łukasik ◽  
Chris Simon ◽  
John P. McCutcheon
Keyword(s):  
Bacterial Endosymbiont ◽  
Periodical Cicadas ◽  
Genome Degradation

scholarly journals Evolutionary Spread and Recombination of Porcine Endogenous Retroviruses in the Suiformes

2005 ◽  
Vol 79 (1) ◽  
pp. 649-654 ◽  
Author(s):  
Marcus Niebert ◽  
Ralf R. Tönjes
Keyword(s):  
Long Terminal Repeat ◽  
Related Species ◽  
Sus Scrofa ◽  
Endogenous Retroviruses ◽  
Phylogenetic Distance ◽  
African Origin ◽  
Closely Related Species ◽  
Separate Event ◽  
Porcine Endogenous Retroviruses ◽  
The Common

ABSTRACT Different Suiformes with increasing phylogenetic distance to the common pig (Sus scrofa) were assayed for the presence of porcine endogenous retroviruses (PERV) in general (pol gene), while the distribution of long terminal repeat (LTR) types (with or without repeats in U3) and env genes (classes A, B, and C) were determined in detail. PERV was not detectable in the most distantly related species, while classes PERV-A and PERV-B are present in Suiformes originating in the Pliocene epoch, and class PERV-C was detectable only in S. scrofa and in closely related species originating in the Holocene epoch. This distribution pattern of PERV classes is in line with our previous study on the age of PERV (45) and suggests an African origin of about 7.5 million years ago (MYA) and a gradual spread of PERV through the Suiformes. It seems likely that PERV-C originated more recently (1.5 to 3.5 MYA) by recombination with a homologue of unknown descent, while the origin of the repeatless LTR was a separate event approximately 3.5 MYA.

scholarly journals Differences in size, structure and function of free and membrane-bound polyribosomes of rat liver. Evidence for a single class of membrane-bound polyribosomes

1977 ◽  
Vol 168 (1) ◽  
pp. 1-8 ◽  
Author(s):  
J C Ramsey ◽  
W J Steele
Keyword(s):  
Protein Synthesis ◽  
Rat Liver ◽  
Size Structure ◽  
Large Fraction ◽  
Liver Homogenate ◽  
Structure And Function ◽  
Structural And Functional Properties ◽  
Membrane Bound ◽  
And Function

Free loosely bound and tightly bound polyribosomes were separated from rat liver homogenate by salt extraction followed by differential centrifugation, and several of their structural and functional properties were compared to resolve the existence of loosely bound polyribosomes and verify the specificity of the separation. The free and loosely bound polyribosomes have similar sedimentation profiles and polyribosome contents, their subunit proteins have similar electrophoretic patterns and their products of protein synthesis in vitro show a close correspondence in size and amounts synthesized. In contrast, the tightly bound polyribosomes have different properties from those of the free and loosely bound polyribosomes; their average size is significantly smaller; their polyribosome content is higher; their 60 S-subunit proteins lack two components and contain four or more components not found elsewhere; their products of protein synthesis in vitro differ in size and amounts synthesized. These observations show that rat liver membranes entrap a large fraction of the free polyribosomes at low salt concentrations and that these polyribosomes are similar to those of the free-polyribosome fraction and are different from those of the tightly bound polyribosome fraction in size, structure and function.

scholarly journals Comparative transcriptomics of the venoms of continental and insular radiations of West African cones

2020 ◽  
Vol 287 (1929) ◽  
pp. 20200794
Author(s):  
Samuel Abalde ◽  
Manuel J. Tenorio ◽  
Carlos M. L. Afonso ◽  
Rafael Zardoya
Keyword(s):  
Related Species ◽  
Common Ancestor ◽  
West African ◽  
Generic Level ◽  
Closely Related Species ◽  
Functional Convergence ◽  
Venom Glands ◽  
Phylogenetic Framework ◽  
The Common ◽  
Secreted Peptides

The transcriptomes of the venom glands of 13 closely related species of vermivorous cones endemic to West Africa from genera Africonus and Varioconus were sequenced and venom repertoires compared within a phylogenetic framework using one Kalloconus species as outgroup. The total number of conotoxin precursors per species varied between 108 and 221. Individuals of the same species shared about one-fourth of the total conotoxin precursors. The number of common sequences was drastically reduced in the pairwise comparisons between closely related species, and the phylogenetical signal was totally eroded at the inter-generic level (no sequence was identified as shared derived), due to the intrinsic high variability of these secreted peptides. A common set of four conotoxin precursor superfamilies (T, O1, O2 and M) was expanded in all studied cone species, and thus, they are considered the basic venom toolkit for hunting and defense in the West African vermivorous cone snails. Maximum-likelihood ancestral character reconstructions inferred shared conotoxin precursors preferentially at internal nodes close to the tips of the phylogeny (between individuals and between closely related species) as well as in the common ancestor of Varioconus . Besides the common toolkit, the two genera showed significantly distinct catalogues of conotoxin precursors in terms of type of superfamilies present and the abundance of members per superfamily, but had similar relative expression levels indicating functional convergence. Differential expression comparisons between vermivorous and piscivorous cones highlighted the importance of the A and S superfamilies for fish hunting and defense.

scholarly journals Common envelope episodes that lead to double neutron star formation

2020 ◽  
Vol 37 ◽  
Author(s):  
Alejandro Vigna-Gómez ◽  
Morgan MacLeod ◽  
Coenraad J. Neijssel ◽  
Floor S. Broekgaarden ◽  
Stephen Justham ◽  
...  
Keyword(s):  
Gamma Ray ◽  
Initial Conditions ◽  
Large Fraction ◽  
Computational Modelling ◽  
Evolutionary Stage ◽  
Population Synthesis ◽  
Radio Pulsars ◽  
Common Envelope ◽  
The Common ◽  
The Moment

Abstract Close double neutron stars (DNSs) have been observed as Galactic radio pulsars, while their mergers have been detected as gamma-ray bursts and gravitational wave sources. They are believed to have experienced at least one common envelope episode (CEE) during their evolution prior to DNS formation. In the last decades, there have been numerous efforts to understand the details of the common envelope (CE) phase, but its computational modelling remains challenging. We present and discuss the properties of the donor and the binary at the onset of the Roche lobe overflow (RLOF) leading to these CEEs as predicted by rapid binary population synthesis models. These properties can be used as initial conditions for detailed simulations of the CE phase. There are three distinctive populations, classified by the evolutionary stage of the donor at the moment of the onset of the RLOF: giant donors with fully convective envelopes, cool donors with partially convective envelopes, and hot donors with radiative envelopes. We also estimate that, for standard assumptions, tides would not circularise a large fraction of these systems by the onset of RLOF. This makes the study and understanding of eccentric mass-transferring systems relevant for DNS populations.

scholarly journals Lack of Adaptation of Chimeric GB Virus B/Hepatitis C Virus in the Marmoset Model: Possible Effects of Bottleneck

2009 ◽  
Vol 83 (16) ◽  
pp. 8062-8075 ◽  
Author(s):  
Trudie Weatherford ◽  
Deborah Chavez ◽  
Kathleen M. Brasky ◽  
Stanley M. Lemon ◽  
Annette Martin ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Common Marmoset ◽  
Serial Passage ◽  
Chimeric Virus ◽  
World Population ◽  
Closely Related Species ◽  
Efficient Replication ◽  
Time Of Infection ◽  
The Common

ABSTRACT Approximately 3% of the world population is chronically infected with hepatitis C virus (HCV). GB virus B (GBV-B), a surrogate model for HCV, causes hepatitis in tamarins and is the virus phylogenetically most closely related to HCV. Previously we described a chimeric GBV-B containing an HCV insert from the 5′ noncoding region (NCR) that was adapted for efficient replication in tamarins (Saguinus species). We have also demonstrated that wild-type (WT) GBV-B rapidly adapts for efficient replication in a closely related species, the common marmoset (Callithrix jacchus). Here, we demonstrate that the chimeric virus failed to adapt during serial passage in marmosets. The chimeric virus was passaged four times through 24 marmosets. During passage, two marmoset phenotypes were observed: susceptible and partially resistant. Although appearing to adapt in a resistant animal during a prolonged and gradual increase in viremia, the chimeric GBV-B failed to replicate efficiently upon passage to a naïve marmoset. The resistance was specific to the chimeric virus, as the chimeric virus-resistant animals were susceptible to marmoset-adapted WT virus during rechallenge studies. Three isolates of the chimeric virus were sequenced, and 20 nucleotide changes were observed, including eight amino acid changes. Three unique changes were observed in the 5′ NCR chimeric insert, an area that is highly conserved in HCV. We speculate that the failure of the chimeric virus to adapt in marmosets might be due to a bottleneck that occurs at the time of infection of resistant animals, which may lead to a loss of fitness upon serial passage.

scholarly journals Population Ecology Studies on Infaunal Polychaetes of Pauatahanui Inlet

2021 ◽  
Author(s):  
◽  
Geoffrey Bernard Read
Keyword(s):  
Size Structure ◽  
Environmental Gradients ◽  
Age Groups ◽  
Differential Mortality ◽  
Intertidal Flat ◽  
Adult Size ◽  
Spawning Period ◽  
Near Surface ◽  
Pair Density ◽  
The Common

<p>Macrofaunal polychaete densities across a stable, fine-sand, intertidal flat in Pauatahanui Inlet were examined from a set of seasonal samples, 500 micron sieve processed, from a stratified transect pair. Density Patterns had shore-normal trends, despite apparently weak tidal-cycle environmental gradients. Zones of high abundance of common species persisted unchanged, but seasonal increase and decline occurred within them, with also some population redistribution attributable to differential mortality/recruitment, or possibly to migration. Correlation analysis did not detect interspecies relationships linked to the abundance and zonation of the common polychaetes, all deposit-feeders. The population dynamics of six species was investigated from the transect-pair seasonal samples, supplemented by subsequent more finely-sieved samples during dense recruitment periods. The maldanid Axiothella serrata had three identifiable age groups O, I, and II+, with I plus II+ density to about 550 m-2. The new O group began to appear in October-November, as aggregates below 3 cm sediment depth, believed to represent lecithotropic, direct-developing, siblings from egg masses of the II+ group. Juvenile setiger-total frequencies indicated synchronous adult spawning occurred at varying intervals during an approximate six month period. Peak density of dispersed, near-surface recruits reached 29 thousand m-2. Setiger-total was the most sensitive indicator of size and age in juveniles of up to about 15 setigers. Zonation patterns were age specific. The predominantly lower-shore capitellid, Heteromastus filiformis had a short summer spawning period with settlement ending before May, when population density was up to 10 thousand m-2. Merger of O group into the adult size range occurred in about one year, and probably first spawning was at the end of the second year, with life span of three years or more. The nereidid Nicon aestuariensis had I+ and older age groups at barely detectable densities. Spawning was probably in late summer although an O group, at about 500 m-2, was not detected until May. The spionid Scolecolepides benhami had apparently unchanging size structure and density (about 400 m-2 transect-wide); new settlement was not detected. High density occurred only in a narrow near-shore strip. Nicon aestuariensis also declined down-shore, but more gradually. The spionid Microspio sp. and capitellid Capitella sp. were short-lived, near-surface species, with apparently continuous recruitment from planktotrophic and direct-development respectively. A spring recruitment increase created at first a separate modal group of juveniles, and raised Microspio sp. density to 45 thousand m-2 and Capitella sp. to 7 thousand m-2. Capitella sp. declined in density downshore, but Microspio sp. was only weakly zoned. The common polychaetes had largely concordant density cycles with settlement (or peak settlement) spring-summer orientated, although 500 micron mesh processing detected the peak of surviving adults in autumn-winter. Pauatahanui polychaetes as an assemblage, life history traits, links between population structure and zonation, and problems in polychaete population studies are discussed.</p>

scholarly journals Spatial inter-centromeric interactions facilitated the emergence of evolutionary new centromeres

2020 ◽  
Author(s):  
Krishnendu Guin ◽  
Yao Chen ◽  
Radha Mishra ◽  
Siti Rawaidah B. M. Muzaki ◽  
Bhagya C. Thimmappa ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Assembly ◽  
Candida Parapsilosis ◽  
Common Ancestor ◽  
Spatial Proximity ◽  
Closely Related Species ◽  
Chromosome Conformation ◽  
3D Genome ◽  
The Common ◽  
Evolutionary New Centromeres

AbstractCentromeres of Candida albicans form on unique and different DNA sequences but a closely related species, Candida tropicalis, possesses homogenized inverted repeat (HIR)-associated centromeres. To investigate the mechanism of centromere-type transition, we improved the fragmented genome assembly and constructed a chromosome-level genome assembly of C. tropicalis by employing PacBio sequencing, chromosome conformation capture sequencing (3C-seq), chromoblot, and genetic analysis of engineered aneuploid strains. Further, we analyzed the 3D genome organization using 3C-seq data, which revealed spatial proximity among the centromeres as well as telomeres of seven chromosomes in C. tropicalis. Intriguingly, we observed evidence of inter-centromeric translocations in the common ancestor of C. albicans and C. tropicalis. Identification of putative centromeres in closely related Candida sojae, Candida viswanathii and Candida parapsilosis indicates loss of ancestral HIR-associated centromeres and establishment of evolutionary new centromeres (ENCs) in C. albicans. We propose that spatial proximity of the homologous centromere DNA sequences facilitated karyotype rearrangements and centromere type transitions in human pathogenic yeasts of the CUG-Ser1 clade.

scholarly journals Longitudinal cell division is associated with single mutations in the FtsZ-recruiting SsgB in Streptomyces

2019 ◽  
Author(s):  
Xiansha Xiao ◽  
Joost Willemse ◽  
Patrick Voskamp ◽  
Xinmeng Li ◽  
Meindert Lamers ◽  
...  
Keyword(s):  
Cell Division ◽  
Biochemical Analysis ◽  
Amino Acid Substitutions ◽  
Free Living ◽  
Division Plane ◽  
Z Ring ◽  
Living Bacterium ◽  
Longitudinal Division ◽  
Longitudinal Cell ◽  
Free Living Bacterium

ABSTRACTIn most bacteria, cell division begins with the polymerization of the GTPase FtsZ at the mid-cell, which recruits the division machinery to initiate cell constriction. In the filamentous bacterium Streptomyces, cell division is positively controlled by SsgB, which recruits FtsZ to the future septum sites and promotes Z-ring formation. Here we show via site-saturated mutagenesis that various amino acid substitutions in the highly conserved SsgB protein result in the production of ectopically placed septa, that sever spores diagonally or along the long axis, perpendicular to the division plane. Ectopic septa were especially prominent when cells expressed SsgB variants with substitutions in residue E120. Biochemical analysis of SsgB variant E120G revealed that its interaction with - and polymerization of - FtsZ had been maintained. The crystal structure of S. coelicolor SsgB was resolved and the position of residue E120 suggests its requirement for maintaining the proper angle of helix α3, thus providing a likely explanation for the aberrant septa formed in SsgB E120 substitution mutants. Taken together, our work presents the first example of longitudinal division in a free living bacterium, which is explained entirely by changes in the FtsZ-recruiting protein SsgB.

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