Cospeciation Between the Primary Endosymbionts of Mealybugs and Their Hosts

Mealybugs have an association with prokaryotic endosymbionts that are located in specialized cells called bacteriocytes. In order to compare the phylogeny of the host with that of the previously published phylogeny of the endosymbionts, 3.1 to 3.2 kilobase DNA fragments containing mitochondrial cytB (part), nd1,16S ribosomal DNA(rDNA), and 12S rDNA (part) were amplified and sequenced. A phylogenetic analysis of the data and a comparison with the trees obtained from endosymbiont genes and host 18S and 28S rDNA indicated that all the trees were similar. This result is consistent with an infection of a mealybug ancestor with a precursor of the endosymbiont followed by the vertical transmission of the endosymbiont to progeny. Comparison of the guanine + cytosine (G + C) contents of the mealybug mitochondrial genes with the same genes from other members of Sternorrhyncha and Arthropoda indicated that the mealybug genes had unusually low G + C contents in their DNAs (10.2 to 11.1 mol%).     

Blattabacteria,the endosymbionts of cockroaches,have small genome sizes and high genome copy numbers

Blattabacteria are intracellular endosymbionts of cockroaches and primitive termites that belong to the class Flavobacteria and live only in specialized cells in the abdominal fat body of their hosts. In the present study we determined genome sizes as well as genome copy numbers for the endosymbionts of three cockroach species, Blattella germanica, Periplaneta americana and Blatta orientalis. The sole presence of blattabacteria in the fat body was demonstrated by rRNA‐targeting techniques. The genome sizes of the three blattabacteria were determined by pulsed field gel electrophoresis. The resulting total genome sizes for the three symbionts were all approximately 650 ± 15 kb. Comparison of the genome sizes with those of free‐living Bacteroidetes shows extended reduction, as occurs in other obligatory insect endosymbionts. Genome copy numbers were determined based on cell counts and determination of DNA amounts via quantitative PCR. Values between 10.2 and 18.3 and between 323 and 353 were found for the symbionts of P. americana and B. orientalis respectively. Polyploidy in intracellular bacteria may play a significant role in the genome reduction process.     

The regulatory region of the L-arabinose operon: its isolation on a 1000 base-pair fragment from DNA heteroduplexes.

A DNA fragment containing the l-arabinose operon regulatory region of Escherichia coli was purified from DNA heteroduplexes formed between opposite strands of two non-defective ara transducing phage. The phage and arabinose gene orientation is such that the heteroduplex contains two single-stranded “bubbles”. The ara regulatory region and short portions of the flanking araB and araC genes are in the short duplex between the “bubbles”. Extensive regions of homology between the phage genomes allowed nearly half of the DNA renatured from a mixture of the two phage DNAs to be in the form of heteroduplexes. Digestion of the reannealed DNA containing heteroduplexes and homoduplexes with the easily purified, single-strand specific nuclease S₁ yielded the 1000 (1017 ± 20, n = 36) base-pair ara DNA duplex plus half and whole phage-length duplexes. The larger DNA duplexes were selectively precipitated by polyethylene glycol before the final purification by preparative electrophoresis on polyacryl-amide gels. By these methods 10 to 20 μg of the 1000 base-pair DNA fragment were purified.     

Tobacco single-copy DNA is highly homologous to sequences present in the genomes of its diploid progenitors

Summary We compared the single-copy DNA sequences of the tetraploid tobacco plant, Nicotiana tabacum, with those of its diploid progenitors N. sylvestris and N. tomentosiformis. We observed that 65% of N. sylvestris and N. tomentosiformis single-copy DNA fragments reacted with each other using moderately stringent hybridization conditions (60° C, 0.18 M Na⁺). An additional 10% sequence homology was detected when the hybridization temperature was reduced by 10° C. The thermal stability of interspecific single-copy DNA duplexes indicated that they were approximately 6% more mispaired than homologous single-copy DNA duplexes. In contrast, we observed almost no single-copy DNA divergence between N. tabacum and its diploid progenitors. Greater than 99% of N. sylvestris and N. tomentosiformis single-copy DNAs reacted with N. tabacum DNA using moderately stringent hybridization conditions. The thermal stability of these duplexes indicated that they contained no more sequence mismatch than homologous single-copy duplexes. Together, our results show that significant single-copy DNA sequence divergence has occurred between the diploid N. sylvestris and N. tomentosiformis genomes. However, by applying our experimental criteria these single-copy DNAs are indistinguishable from their counterparts in the hybrid N. tabacum nucleus.     

Endosymbiont metacommunities,mtDNA diversity and the evolution of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex

Bemisia tabaci, an invasive pest that causes crop damage worldwide, is a highly differentiated species complex, divided into biotypes that have mainly been defined based on mitochondrial DNA sequences. Although endosymbionts can potentially induce population differentiation, specialization and indirect selection on mtDNA, studies have largely ignored these influential passengers in B. tabaci, despite as many as seven bacterial endosymbionts have been identified. Here, we investigate the composition of the whole bacterial community in worldwide populations of B. tabaci, together with host genetic differentiation, focusing on the invasive B and Q biotypes. Among 653 individuals studied, more than 95% of them harbour at least one secondary endosymbiont, and multiple infections are very common. In addition, sequence analyses reveal a very high diversity of facultative endosymbionts in B. tabaci, with some bacterial genus being represented by more than one strain. In the B and Q biotypes, nine different strains of bacteria have been identified. The mtDNA‐based phylogeny of B. tabaci also reveals a very high nucleotide diversity that partitions the two ITS clades (B and Q) into six CO1 genetic groups. Each genetic group is in linkage disequilibrium with a specific combination of endosymbionts. All together, our results demonstrate the rapid dynamics of the bacterial endosymbiont–host associations at a small evolutionary scale, questioning the role of endosymbiotic communities in the evolution of the Bemisia tabaci species complex and strengthening the need to develop a metacommunity theory of inherited endosymbionts.     

Evidence for Multiple Acquisition of <Emphasis Type="Italic">Arsenophonus</Emphasis> by Whitefly Species (Sternorrhyncha: Aleyrodidae)

Whiteflies contain primary prokaryotic endosymbionts located within specialized host cells. This endosymbiotic association is the result of a single infection of the host followed by vertical transmission of the endosymbiont to the progeny. Whiteflies may also be associated with other bacteria called secondary (S-) endosymbionts. The nucleotide sequence of the 16S–23S ribosomal DNA from S-endosymbionts of 13 whitefly species was determined. A phylogenetic analysis of these sequences indicated their grouping into two major clusters, one consisting of two S-endosymbionts related to previously described T-type endosymbionts. The second cluster contained the 16S–23S rDNA sequence of the type strain of Arsenophonus nasoniae as well as sequences of S-endosymbionts from 11 whitefly species. This Arsenophonus cluster contained four S-endosymbionts with intervening sequences of 70–184 nucleotides in their 23S rDNAs. The phylogenetic tree of the Arsenophonus cluster differed greatly from the phylogenetic tree of the primary endosymbionts. These results suggest that, unlike the primary endosymbiont, Arsenophonus may infect whiteflies multiple times and may also be horizontally transmitted.     

Host genotype–endosymbiont associations and their relationship with aphid parasitism at the field level

1. The relationship between endosymbionts and insects represent complex eco‐evolutionary interactions. Vertically transmitted endosymbionts can be a source of evolutionary novelty by conferring ecologically important traits to their insect hosts, such as protection against natural enemies. Host–endosymbiont associations could constitute an adaptive complex (holobiont) on which selective pressures present in the environment can act, being transferred to the next generation. 2. Although several laboratory‐based studies have confirmed host genotype × symbiont interactions, few studies have been directed at those associations in the natural populations and their ability to protect themselves from parasitism pressure at the field level. 3. A field‐based approach to study the aphid genotype–endosymbiont associations and its relationship with the total parasitism in the grain aphid Sitobion avenae was conducted. From the field study, experiments were carried out to study the defensive effect of the two most common facultative endosymbionts (Regiella insecticola and Hamiltonella defensa) present in S. avenae against one of the most important parasitoid species, Aphidius ervi. 4. Evidence is presented here of a high specificity of the aphid clone–endosymbiont associations in the field; however, the field and experimental results here do not support a relationship between the aphid clone–endosymbiont associations and a proxy of total parasitism in S. avenae. These findings highlight the importance of particular host clone–endosymbiont couplings as a key factor in gaining an understanding of the coevolutionary dynamics of endosymbionts in nature and their effect on the invasive potential of pest insects.     

Molecular diversity of bacterial endosymbionts associated with dagger nematodes of the genus Xiphinema (Nematoda: Longidoridae) reveals a high degree of phylogenetic congruence with their host

Bacterial endosymbionts have been detected in some groups of plant‐parasitic nematodes, but few cases have been reported compared to other groups in the phylum Nematoda, such as animal‐parasitic or free‐living nematodes. This study was performed on a wide variety of plant‐parasitic nematode families and species from different host plants and nematode populations. A total of 124 nematode populations (previously identified morphologically and molecularly) were screened for the presence of potential bacterial endosymbionts using the partial 16S rRNA gene and fluorescence in situ hybridization (FISH) and confocal microscopy. Potential bacterial endosymbionts were only detected in nematode species belonging to the genus Xiphinema and specifically in the X. americanum group. Fifty‐seven partial 16S rRNA sequences were obtained from bacterial endosymbionts in this study. One group of sequences was closely related to the genus ‘Candidatus Xiphinematobacter’ (19 bacterial endosymbiont sequences were associated with seven nematode host species, including two that have already been described and three unknown bacterial endosymbionts). The second bacterial endosymbiont group (38 bacterial endosymbiont sequences associated with six nematode species) was related to the family Burkholderiaceae, which includes fungal and soil–plant bacterial endosymbionts. These endosymbionts were reported for the first time in the phylum Nematoda. Our findings suggest that there is a highly specific symbiotic relationship between nematode host and bacterial endosymbionts. Overall, these results were corroborated by a phylogeny of nematode host and bacterial endosymbionts that suggested that there was a high degree of phylogenetic congruence and long‐term evolutionary persistence between hosts and endosymbionts.     

Related base sequences in the DNA of simple and complex organisms. V. The specificity of interactions between oligonucleotides and denatured DNA

A mixture of differentially labeled mouse and Bacillus subtilis DNA was used as a source of oligodeoxynucleotides of chain lengths from 15 to 40 nucleotides. The extent of interaction of these oligonucleotides with homologous or heterologous DNA bound to membrane filters was measured. The specificity of such interactions increases with chain length and with the incubation temperature. The thermal stability of the complexes is a function of chain length. Homologous oligonucleotide/DNA duplexes of B. subtilis are more stable than those of mouse of corresponding size, consistent with the incidence of partially related base sequences in mouse DNA. Oligonucleotides in this size range are also able to recognize partially complementary base sequences in the DNA of closely related organisms. This approach shows promise as a means of obtaining quantitative estimates of base sequence divergence between the DNAs of related organisms.This research was supported by a grant from the National Science Foundation (GB 6099).     

Effects of antibiotics on fitness of the B biotype and a non-B biotype of the whitefly Bemisia tabaci

The whitefly, Bemisia tabaci Gennadius (Homoptera: Aleyrodidae), harbors primary and secondary endosymbionts. Previous research showed that the invasive B biotype and an indigenous non‐B biotype (named non‐B ZHJ‐1 population) of B. tabaci from Zhejiang, China, harbored different endosymbionts. To investigate the function of these endosymbionts in the two biotypes of B. tabaci, we fed adult whiteflies with three antibiotics, tetracycline, ampicillin trihydrate, and rifampicin, and evaluated the fitness of their offspring on cotton plants. These three antibiotics did not remove the primary endosymbiont Portiera aleyrodidarum but were capable of eliminating the secondary endosymbionts. In the B biotype, treatments of adults with tetracycline or ampicillin trihydrate accelerated development and increased the survival of their offspring, while treatment of adults with rifampicin significantly retarded the development of their offspring but did not affect their survival. In the non‐B ZHJ‐1 population, treatments of adults with tetracycline or ampicillin trihydrate also accelerated the development of their offspring but did not significantly affect their survival, while treatment of adults with rifampicin significantly retarded development and reduced the survival of their offspring. These results suggest that removal of some secondary endosymbionts and/or reduction of the primary endosymbiont from B. tabaci may produce both favorable and unfavorable effects on the fitness of the host insects.     

Serial replacement of a diatom endosymbiont in the marine dinoflagellate Peridinium quinquecorne (Peridiniales, Dinophyceae)

To infer the phylogeny of both the host and the endosymbiont of Peridinium quinquecorne Abé, the small subunit (SSU) ribosomal DNA (rDNA) from the host and two genes of endosymbiont origin (plastid‐encoded rbcL and nuclear‐encoded SSU rDNA) were determined. The phylogenetic analysis of the host revealed that the marine dinoflagellate P. quinquecorne formed a clade with other diatom‐harbouring dinoflagellates, including Kryptoperidinium foliaceum (Stein) Lindeman, Durinskia baltica (Levander) Carty et Cox and Galeidinium rugatum Tamura et Horiguchi, indicating a single endosymbiotic event for this lineage. Phylogenetic analyses of the endosymbiont in these organisms revealed that the endosymbiont of P. quinquecorne formed a clade with a centric diatom (SSU data indicated it to be closely related to Chaetoceros), whereas the endosymbionts of other three dinoflagellates formed a clade with a pennate diatom. The discrepancy between the host and the endosymbiont phylogenies suggests a secondary replacement of the endosymbiont from a pennate to a centric diatom in P. quinquecorne.     

Cospeciation of Psyllids and Their Primary Prokaryotic Endosymbionts

Psyllids are plant sap-feeding insects that harbor prokaryotic endosymbionts in specialized cells within the body cavity. Four-kilobase DNA fragments containing 16S and 23S ribosomal DNA (rDNA) were amplified from the primary (P) endosymbiont of 32 species of psyllids representing three psyllid families and eight subfamilies. In addition, 0.54-kb fragments of the psyllid nuclear gene wingless were also amplified from 26 species. Phylogenetic trees derived from 16S-23S rDNA and from the host wingless gene are very similar, and tests of compatibility of the data sets show no significant conflict between host and endosymbiont phylogenies. This result is consistent with a single infection of a shared psyllid ancestor and subsequent cospeciation of the host and the endosymbiont. In addition, the phylogenies based on DNA sequences generally agreed with psyllid taxonomy based on morphology. The 3′ end of the 16S rDNA of the P endosymbionts differs from that of other members of the domain Bacteria in the lack of a sequence complementary to the mRNA ribosome binding site. The rate of sequence change in the 16S-23S rDNA of the psyllid P endosymbiont was considerably higher than that of other bacteria, including other fast-evolving insect endosymbionts. The lineage consisting of the P endosymbionts of psyllids was given the designation Candidatus Carsonella (gen. nov.) with a single species, Candidatus Carsonella ruddii (sp. nov.).     

Aspects of energy-yielding metabolism in the aphid,Schizaphis graminum,and its endosymbiont: Detection of gene fragments potentially coding for the ATP synthaseβ-subunit and glyceraldehyde-3-phosphate dehydrogenase

Specialized cells within the aphid,Schizaphis graminum, contain intracellular, vesicleenclosed eubacterial endosymbionts (Buchnera aphidicola). Using oligonucleotide probes derived from conserved sequences of the ATP synthase -subunit and glyceraldehyde-3-phosphate dehydrogenase, and the polymerase chain reaction (PCR), we have amplified, cloned, and sequenced three DNA fragments. Amino acid sequence similarity indicated that two of these fragments corresponded to endosymbiont and host genes potentially coding for the -subunit of ATP synthase. The host gene fragment contained two putative introns. The third DNA fragment corresponded to a portion of a gene coding for a glyceraldehyde-3-phosphate dehydrogenase that was highly related to one of the enzymes fromEscherichia coli (GapA). These results indicate thatB. aphidicola may have an ATP synthase and consequently could synthesize ATP from a proton motive force generated within the intracellular vesicles of host cells containing the endosymbionts. The detection of a gene fragment coding for a protein similar to glyceraldehyde-3-phosphate dehydrogenase suggests the presence of this glycolytic enzyme in the endosymbiont and its involvement in energy-yielding metabolism.     

Sequence Analysis of DNA Fragments from the Genome of the Primary Endosymbiont of the Whitefly <Emphasis Type="Italic">Bemisia tabaci</Emphasis>

The whitefly Bemisia tabaci contains a primary prokaryotic endosymbiont housed within specialized cells in the body cavity. Two DNA fragments from the endosymbiont, totaling 33.3 kilobases, were cloned and sequenced. In total, 37 genes were detected and included the ribosomal RNA operon and genes for ribosomal RNA proteins. The guanine plus cytosine of the DNA was 30.2 mol%, different from that of endosymbionts of other plant sap-sucking insects.     

Effects of different temperature regimes on survival of Diaphorina citri and its endosymbiotic bacterial communities

The Asian citrus psyllid, Diaphorina citri, is a major pest of citrus and vector of citrus greening (huanglongbing) in Asian. In our field‐collected psyllid samples, we discovered that Fuzhou (China) and Faisalabad (Pakistan), populations harbored an obligate primary endosymbiont Candidatus Carsonella (gen. nov.) with a single species, Candidatus Carsonella ruddii (sp. nov.) and a secondary endosymbiont, Wolbachia surface proteins (WSP) which are intracellular endosymbionts residing in the bacteriomes. Responses of these symbionts to different temperatures were examined and their host survival assessed. Diagnostic PCR assays showed that the endosymbionts infection rates were not significantly reduced in both D. citri populations after 24 h exposure to cold or heat treatments. Although quantitative PCR assays showed significant reduction of WSP relative densities at 40°C for 24 h, a substantial decrease occurred as the exposure duration increased beyond 3 days. Under the same temperature regimes, Ca. C. ruddii density was initially less affected during the first exposure day, but rapidly reduced at 3–5 days compared to WSP. However, the mortality of the psyllids increased rapidly as exposure time to heat treatment increased. The responses of the two symbionts to unfavorable temperature regimes highlight the complex host‐symbionts interactions between D. citri and its associated endosymbionts.     

EFFECTS OF NITROGEN AND PHOSPHORUS ON THE ENDOSYMBIONT LOAD OF RHOPALODIA GIBBA AND EPITHEMIA TURGIDA (BACILLARIOPHYCEAE)1

Diatoms of the family Epithemiaceae possess a unicellular nitrogen-fixing cyanobacterial endosymbiont. We investigated the potential of extracellular nitrogen and phosphorus concentrations to affect the endosymbiont load of Rhopalodia gibba O. Müll, and Epithemia turgida Ehr. in field and culture populations. In a growth chamber experiment, monoclonal cultures of R. gibba were exposed to three levels of nitrate-nitrogen. Nutrient-diffusing substrates were used in a lake environment to create nine microhabitats of varying nitrogen and phosphorus ratios for natural populations of R. gibba and E. turgida. The number of endosymbionts per diatom increased as ambient nitrogen became limiting; mean endosymbiont volume increased as nitrogen increased. The mean endosymbiont surface area: volume ratio decreased with increasing nitrogen. Total endosymbiont volume per diatom (the product of the number of endosymbionts per diatom and their individual biovolumes) did not have a simple response to increasing nitrogen. Phosphorus limitation uncoupled the relationship between endosymbiont load and nitrogen. We suspect that flexibility of the endosymbiont load can reduce the metabolic cost to the diatom if the endosymbionts are dependent on the diatom for a resource.     

Thermal stability of homologous and heterologous bacterial DNA duplexes

Thermal stability of homologous and heterologous DNA duplexes renatured according to the renaturation-rate method of De Ley et al. (1970) for 35 min or 17 hr, was estimated from the melting profiles of the duplexes. Comparison of the melting points of native and renatured DNA revealed that in the first 35 min of renaturation highly stable homologous duplexes were mainly formed, whereas up to 7% mismatching occurred in duplexes renatured for 17 hr. Up to 8% more mismatching was found in heterologous DNA duplexes of moderately related coryneform bacteria than in homologous ones after 35 min renaturation. It can be concluded that mismatching in heterologous hybrids of closely related DNAs had been restricted to a few % and of moderately related DNAs to approximately 10% in the initial renaturation phase.     

Single-stranded DNA versus tailed duplex in sequence conversion of lacZα DNA

Abstract

Targeted DNA editing has great potential to cure some genetic diseases; however, the use of artificial nucleases such as CRISPR-Cas9 and TALEN in gene therapy can potentially cause severe side effects due to off-target DNA cleavages. Single-stranded (ss) DNAs and 5'-tailed duplexes (TDs) can achieve target base substitutions when introduced without artificial nucleases into cultured cells and mouse liver. In this study, ss DNA and TD were separately co-introduced into human U2OS cells, together with a target plasmid DNA bearing an inactivated lacZα gene, and the gene correction efficiencies were compared. Unlike the genes examined in previous studies, ss DNA and TD showed similar efficiencies. Therefore, ss DNAs might be as useful as TD for gene correction, depending on the target sequence.     

DNA repair and the evolution of transformation IV. DNA damage increases transformation

Natural genetic transformation in the bacterium Bacillus subtilis provides a model system to explore the evolutionary function of sexual recombination. In the present work, we study the response of transformation to UV irradiation using donor DNAs that differ in sequence homology to the recipient's chromosome and in the mechanism of transformation. The four donor DNAs used include homologous-chromosomal-DNA, two plasmids containing a fragment of B. subtilis trp⁺ operon DNA and a plasmid with no sequence homology to the recipient cell's DNA. Transformation frequencies for these DNA molecules increase with increasing levels of DNA damage (UV radiation) to recipient cells, only if their transformation requires homologous recombination (i.e. is recA⁺-dependent). Transformation with non-homologous DNA is independent of the recipient's recombination system and transformation frequencies for it do not respond to increases in UV radiation. The transformation frequency for a selectable marker increases in response to DNA damage more dramatically when the locus is present on small, plasmid-borne, homologous fragments than if it is carried on high molecular weight chromosomal fragments. We also study the kinetics of transformation for the different donor DNAs. Different kinetics are observed for homologous transformation depending on whether the homologous locus is carried on a plasmid or on chromosomal fragments. Chromosomal DNA- and non-homologous-plasmid-DNA-mediated transformation is complete (maximal) within several minutes, while transformation with a plasmid containing homologous DNA is still occurring after an hour. The results indicate that DNA damage directly increases rates of homologous recombination and transformation in B. subtilis. The relevance of these results and recent results of other labs to the evolution of transformation are discussed.     

A guanine-linked end-effect is a sensitive reporter of charge flow through DNA and RNA double helices

The property of charge (electron hole) flow in DNA duplexes has been the subject of intensive study. RNA-DNA heteroduplexes have also been investigated; however, little information exists on the conductive properties of purely RNA duplexes. In investigating the relative conductive properties of a three molecule DNA-DNA duplex design, using piperidine and aniline to break strands at modified bases, we observed that duplexes with guanine-rich termini generated a large oxidative end-effect, which could serve as a highly sensitive reporter of charge flow through the duplexes. The end-effect was found faithfully to report attenuations in charge flow due to certain single-base mismatches within a duplex. Comparative charge flow experiments on DNA-DNA and RNA-RNA duplexes found large end-effects from both, suggesting that the A and B family of double helices conduct charge comparably. The sheer magnitude of the end-effect, and its high sensitivity to helical imperfections, suggest that it may be exploited as a sensitive reporter for DNA mismatches, as well as a versatile device for studying the structure, folding, and dynamics of complexly folded RNAs and DNAs.