Molecular clocks and evolutionary relationships: possible distortions due to horizontal gene flow

Modeling the mosaic structure of bacterial genomes to infer their evolutionary history

The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.

PHYLOGENETIC ESTIMATION OF PLASMID EXCHANGE IN BACTERIA

The existence of differential horizontal gene transfer may be assessed by comparing the phylogenetic trees derived from two different genes. We use this concept to estimate quantitatively the amount of plasmid exchange that has occurred in a bacterial population. By means of computer simulations we studied the effect of gene transfer on the topological distortion between two phylogenetic trees: one obtained from an euchromosomal gene and another from a plasmid-borne sequence, which may be subjected to horizontal transfer. The basic assumptions of our simulations were (a) that plasmid exchange had occurred recently (after the last population split); and (b) that either the amount of chromosomal horizontal exchange was negligible or that it was only a fraction of the amount of plasmid exchange in which case we will be estimating relative amounts of plasmid transfer. We found that the topological difference between two such trees is a function of the number of plasmid exchange events that have occurred. It can be explained by a logistic model that relates the average distortion index between two trees (d_T ) to the number of transfer events (x). The behavior remains the same under different conditions that were tested (symmetry of the topology, number of taxa in the tree, effect of reconstruction errors, mutation after plasmid transfer). We have also tried our method on empirical data from the literature and estimated the amount of gene transfer that may have occurred among Sym plasmids in agricultural field populations of Rhizobium leguminosarum biovar phaseoli. We found that between 15.77 to 29.98% of all genetic types in these populations have been either the source or the target of a plasmid transfer event. When the comparisons were made among trees derived exclusively from plasmid probes this value dropped to 2.00%. Phylogenetic trees derived from symbiotic and nonsymbiotic sequences were also used to infer the number of gene transfer events among 11 isolates from R. galegae. The estimated number of transfer events of symbiotic sequences was 10.515 (although we do not know out of how many genetic types). We concluded that intraspecific transfer of symbiotic sequences is widespread in these two species of the genus Rhizobium.

Darwinian evolution in the light of genomics

Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

Evolution of multiple families of non-LTR retrotransposons in phlebotomine sandflies

In this paper we report on the diversity and distribution of a set of non-LTR retrotransposon (RTP) reverse transcriptase (RT) sequences isolated from phlebotomine sandflies, and their potential for investigating the evolutionary histories of members of this subfamily of flies (Diptera:Psychodidae, Phlebotominae). The phlebotomine RT sequence families derived from one species were as different from each other as they were from RT sequences derived from other species. When each was used to probe Southern blots of sandfly genomic DNA they hybridized only to the species of source and, usually, to others of the same subgenus, but not to DNA from other subgenera-a hybridization pattern consistent with vertical evolution. There was considerable intraspecific variation in hybridization pattern, suggesting the RTs were part of non-LTR RTPs that are (or were recently) subject to flux in genomic position and copy number. Most of the RT families detected in phlebotomines are monophyletic with respect to previously described RTs, and all are monophyletic with RTs of the F/Jockey (Drosophila melanogaster) type of RTP. Orthologous sequences were isolated from the closely related species Phlebotomus perniciosus and P. tobbi (subgenus Larroussius), and different populations of P. perniciosus. The level of sequence divergence among these orthologous RTs, the subgeneric distribution of each RT family, and the intraspecific variation in hybridization pattern of many of them, indicate this class of sequence will provide genetic markers at the sub-generic level.

Phylogenetic evidence for horizontal transfer of an intervening sequence between species in a spirochete genus

The 23S rRNA genes (rrl genes) of some strains of certain species of the spirochete genus Leptospira carry an intervening sequence (IVS) of 485 to 759 bases flanked by terminal inverted repeat and encoding an open reading frame for a putative protein of over 120 amino acids. The structure and the sporadic distribution of the IVS suggest that it might be a mobile element that can be horizontally transferred within or between species. Phylogenetic hypotheses based on the sequences for six IVS open reading frames from various species were compared with hypotheses constructed by using DNA sequences from the 16S rRNA gene (rrs), which is not closely linked to rrl in this genus. The predicted phylogenies for the IVS and rrs differed in a major respect: one strain that claded with L. weillii in the tree based on the rrs data claded with L. noguchi in the tree based on the IVS data. Neither set of data supported a tree in which this strain was constrained to be in the same clade as was supported by the other set of data. This result indicates a probable horizontal transfer of the IVS from a recent ancestor of L. noguchi to a recent ancestor of one of the L. weillii strains. This observation is the first indication of horizontal transfer of elements encoded on the chromosomes of spirochetes.

Promoter activity of the 1731 Drosophila retrotransposon in a human monocytic cell line

The resemblance between retrotransposons and retroviruses suggests an evolutionary relationship and indicates that they may share common transcription factors. We have analyzed the behaviour of the Drosophila 1731 retrotransposon promoter in the human monocytic U937 cell line. We show that the long terminal repeat (LTR) of 1731 promotes CAT (chloramphenicol acetyl transferase) activity in these cells, in which it is enhanced by phorbol esters. Using gel mobility assays, we detected a human nuclear protein that binds in the U3 region of the LTR in a sequence-specific manner. Its precise target was determined by a DNase I footprinting experiment.

Evolutionary comparisons of three enzymes of the threonine biosynthetic pathway among several microbial species

As an approach in the study of the evolution of threonine biosynthetic pathways throughout various organisms, the sequences of three enzymes, namely homoserine dehydrogenase, homoserine kinase and threonine synthase, originating from six organisms, namely Escherichia coli, Bacillus subtilis, Corynebacterium glutamicum, Brevibacterium lactofermentum, Pseudomonas aeruginosa and Saccharomyces cerevisiae, were compared. As a general trend all three enzymatic activities were carried out by proteins sharing sequence relatedness (except for the homoserine kinase of P aeruginosa). Unexpectedly however, for each step one or two enzymes stood out of the main stream: i) for homoserine dehydrogenase, the yeast protein is atypically similar to the E coli enzyme; ii) for homoserine kinase, the P aeruginosa protein shares no similarity with any other species; and iii) for threonine synthase, the B subtilis protein is far distant from the enzymes of other species. Hence in contrast to other biosynthetic pathways such as the tryptophan one, the threonine pathway seems not to have evolved as a whole throughout different organisms but rather each step seems to have been subjected to multiple constraints including substrate-mediated ones and host-specific ones.

Imported sequences in the mitochondrial yeast genome identified by nucleotide linguistics

In addition to universally appearing mitochondrial (mt) genes, origins of replication and transcription start regions typical of all mt genome variants of the yeast Saccharomyces cerevisiae, the mt genomes of some of the strains contain variable sequences. These sequences are apparently largely dispensable. They are mainly composed of group-I and -II introns and intergenic open reading frames (ORFs). Many of the introns contain ORFs, some of which were shown by genetic and biochemical means to be involved in splicing and transposition of the mt introns. Some of the optional sequences are hypothesized to be mobile genetic elements. Nucleotide (nt) sequences of the mt genome of S. cerevisiae were examined by analyzing occurrences of oligodeoxyribonucleotide (oligo) 'words'. This linguistic technique had been found to be sensitive to both function and origin of the sequence [Pietrokovski et al., J. Biomol. Struct. Dyn. 7 (1990) 1251-1268]. A clear difference is found between the oligo vocabularies of the optional and basic yeast mt sequences. The difference is mainly located in protein coding segments of the optional sequences which contain conserved amino acid motifs, characteristic of intronic and intergenic ORFs. The use of nt linguistics to detect the sequence dissimilarity and its causes in yeast mitochondria provides fast and straightforward results, identifying the intronic and intergenic ORFs as DNA sequences of foreign, non-mt origin.

Cloning and genetic analyses of two highly polymorphic, moderately repetitive nuclear DNAs from Phytophthora infestans

Randomly selected clones from a Phytophthora infestans partial genomic library were characterized by hybridizing individual clones to Southern blots of total genomic DNA digested with the restriction enzyme EcoRI. Among 59 clones that were screened on seven different central-Mexican isolates, five revealed a unique banding pattern for each isolate tested. Two of these clones were tested further; the banding patterns produced by both were somatically stable when probed to DNA from 63 single-zoospore (asexual) progeny from five different "parent" isolates. For one probe, RG57, each band appeared to represent a unique genetic locus in three different crosses, and each locus segregated for the presence or absence of a band. No bands were found to be allelic, but two pairs of cosegregating loci were identified. Genetic analyses of the other probe (RG7) revealed many more pairs of cosegregating bands and some bands which were allelic. When these probes were hybridized to DNA from the other five species in Phytophthora group IV, probe RG57 hybridized strongly to DNA from P. colocasiae, P. phaseoli and P. mirabilis, but weakly or not at all to that of P. hibernalis and P. ilicis. Probe RG7 hybridized fairly strongly to DNA from all six species. Because the sequence recognized by probe RG57 appears to be evolutionarily conserved, and is dispersed, moderately repetitive and highly polymorphic, it could be very useful in additional studies on the genetics and population biology of P. infestans.

Distribution of an L-isoaspartyl protein methyltransferase in eubacteria

A protein carboxyl methyltransferase (EC 2.1.1.77) that recognizes age-damaged proteins for potential repair or degradation reactions has been found in all vertebrate tissues and cells examined to date. This enzyme catalyzes the transfer of methyl groups from S-adenosylmethionine to the carboxyl groups of D-aspartyl or L-isoaspartyl residues that are formed spontaneously from normal L-aspartyl and L-asparaginyl residues. A similar methyltransferase has been found in two bacterial species, Escherichia coli and Salmonella typhimurium, suggesting that this enzyme performs an essential function in all cells. In this study, we show that this enzyme is present in cytosolic extracts of six additional members of the alpha and gamma subdivisions of the purple bacteria: Pseudomonas aeruginosa (gamma), Rhodobacter sphaeroides (alpha), and the gamma enteric species Klebsiella pneumoniae, Enterobacter aerogenes, Proteus vulgaris, and Serratia marcescens. DNA probes from the E. coli methyltransferase gene hybridized only to the chromosomal DNA of the enteric species. Interestingly, no activity was found in the plant pathogen Erwinia chrysanthemi, a member of the enteric family, nor in Rhizobium meliloti or Rhodopseudomonas palustris, two members of the alpha subdivision. Additionally, we could not detect activity in the four gram-positive species Bacillus subtilis, B. stearothermophilus, Lactobacillus casei, and Streptomyces griseus. The absence of enzyme activity was not due to the presence of inhibitors in the extracts. These results suggest that many cells may not have the enzymatic machinery to recognize abnormal aspartyl residues by methylation reactions. Since the nonenzymatic degradation reactions that generate these residues occur in all cells, other pathways may be present in nature to ensure that these types of altered proteins do not accumulate and interfere with normal cellular physiology.

Genetics of gene transfer between species

Bacteria transfer genetic information to members of at least three of the five biological kingdoms. Gene transfer between species may play the same role as sex between members of a single species, providing genetic diversity and material for repair of genomic damage.

Cloning and characterization of cDNAs encoding a novel cyclic AMP-binding protein in Dictyostelium discoideum

The cellular slime mould, Dictyostelium discoideum, contains a novel cyclic AMP-binding protein, CABP1, which is composed of two subunits. Using anti-CABP1 monoclonal antibody as a probe, a cDNA clone was isolated from a lambda gt11 expression library. By hybrid selection of the complementary mRNA and its translation in vitro, we demonstrated that the cDNA hybridized to mRNAs encoding both CABP1 polypeptides. With the positive cDNA as a probe, we isolated a series of overlapping cDNA clones covering the coding region of both CABP1 mRNAs. Expression of the cloned cDNAs in bacteria and sequence analysis showed that the CABP1 subunits are identical in amino acid (aa) sequence, except that the small subunit is missing 37 aa near its N terminus. Genomic analysis suggested that the two CABP1 transcripts are derived from a single gene. The N-terminal half of each subunit is rich in proline, glutamine and glycine residues and contains a large block of aa repeats. The C-terminal half has an approx. 47% aa identity (86% with functionally conservative substitutions) with two polypeptides encoded by a plasmid determinant for tellurium anion resistance.

Phylogenetic distribution of the novel avian endogenous provirus family EAV-0

A new family of related endogenous proviruses, existing at 50 to 100 copies per haploid genome and distinguishable by remarkably short long terminal repeats, has been described for domestic chickens (Gallus gallus subsp domesticus). In this communication, by using Southern blot analysis and probes derived from both internal viral sequences and locus-specific, cellular flanking sequences, we studied the genetic distribution of this family of moderately repetitive avian endogenous retroviruses within the genomes of four Gallus species. Eight inbred lines of domestic chickens, the evolutionary progenitor to the domestic chicken (red jungle fowl), and two more distantly related species (grey and green jungle fowl) were studied. All Gallus species harbored this class of elements, although the different lines of domestic chickens and different species of jungle fowl bore distinguishable complements of the proviral loci. Jungle fowl appeared to have fewer copies than domestic chickens. For three randomly isolated proviral loci, domestic chickens (G. gallus subsp. domesticus) and red jungle fowl (G. gallus subsp. gallus) showed only a proviral state, whereas the most primitive and divergent of the jungle fowl, the green jungle fowl (G. varius), consistently demonstrated only preintegration states or disparate alleles. The presence of this family in all Gallus species and of related sequences in other genera suggests that a primordial founding integration event occurred prior to the evolutionary separation of Gallus species and possibly related genera. Additionally, at least one proviral locus has been acquired subsequent to speciation, indicating that this family was actively infectious after the primary founding event. This conserved, repetitive proviral family appears to represent the vestigial remnant of an avian retrovirus class related to and evolutionarily more ancient than the Rous-associated virus-0 family of avian endogenous retroviruses.

Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast

Conjugative plasmids of Escherichia coli can mobilize DNA transmission from this bacterium to the yeast Saccharomyces cerevisiae. The process shares some of the features of conjugation between bacteria and could be evolutionarily significant in promoting trans-kingdom genetic exchange.