Howard Ochman

Lateral gene transfer and the nature of bacterial innovation

Unlike eukaryotes, which evolve principally through the modification of existing genetic information, bacteria have obtained a significant proportion of their genetic diversity through the acquisition of sequences from distantly related organisms. Horizontal gene transfer produces extremely dynamic genomes in which substantial amounts of DNA are introduced into and deleted from the chromosome. These lateral transfers have effectively changed the ecological and pathogenic character of bacterial species.

Sex and virulence in Escherichia coli: an evolutionary perspective.

Pathogenic Escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non‐pathogenic E. coli constitute part of the normal intestinal flora of healthy mammals and birds. The evolutionary pathways underlying this dichotomy in bacterial lifestyle were investigated by multilocus sequence typing of a global collection of isolates. Specific pathogen types [enterohaemorrhagic E. coli, enteropathogenic E. coli, enteroinvasive E. coli, K1 and Shigella] have arisen independently and repeatedly in several lineages, whereas other lineages contain only few pathogens. Rates of evolution have accelerated in pathogenic lineages, culminating in highly virulent organisms whose genomic contents are altered frequently by increased rates of homologous recombination; thus, the evolution of virulence is linked to bacterial sex. This long‐term pattern of evolution was observed in genes distributed throughout the genome, and thereby is the likely result of episodic selection for strains that can escape the host immune response.

Evolution in bacteria: evidence for a universal substitution rate in cellular genomes.

This paper constructs a temporal scale for bacterial evolution by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts. One thus obtains a relationship between time and bacterial RNA divergence which can be used to estimate times of divergence between other branches in the bacterial tree. According to this approach, Salmonella typhimurium and Escherichia coli diverged between 120 and 160 million years (Myr) ago, a date which fits with evidence that the chief habitats occupied now by these two enteric species became available that long ago. The median extent of divergence between S. typhimurium and E. coli at synonymous sites for 21 kilobases of protein-coding DNA is 100%. This implies a silent substitution rate of 0.7-0.8%/Myr--a rate remarkably similar to that observed in the nuclear genes of mammals, invertebrates, and flowering plants. Similarities in the substitution rates of eucaryotes and procaryotes are not limited to silent substitutions in protein-coding regions. The average substitution rate for 16S rRNA in eubacteria is about 1%/50 Myr, similar to the average rate for 18S rRNA in vertebrates and flowering plants. Likewise, we estimate a mean rate of roughly 1%/25 Myr for 5S rRNA in both eubacteria and eucaryotes. For a few protein-coding genes of these enteric bacteria, the extent of silent substitution since the divergence of S. typhimurium and E. coli is much lower than 100%, owing to extreme bias in the usage of synonymous codons. Furthermore, in these bacteria, rates of amino acid replacement were about 20 times lower, on average, than the silent rate. By contrast, for the mammalian genes studied to date, the average replacement rate is only four to five times lower than the rate of silent substitution.

Deletional bias and the evolution of bacterial genomes

Although bacteria increase their DNA content through horizontal transfer and gene duplication, their genomes remain small and, in particular, lack nonfunctional sequences. This pattern is most readily explained by a pervasive bias towards higher numbers of deletions than insertions. When selection is not strong enough to maintain them, genes are lost in large deletions or inactivated and subsequently eroded. Gene inactivation and loss are particularly apparent in obligate parasites and symbionts, in which dramatic reductions in genome size can result not from selection to lose DNA, but from decreased selection to maintain gene functionality. Here we discuss the evidence showing that deletional bias is a major force that shapes bacterial genomes.

Pathogenicity Islands: Bacterial Evolution in Quantum Leaps

Is the acquisition of a pathogenicity island sufficient to transform an organism into a pathogen? Three factors determine the virulence role of pathogenicity islands: the genes within the island, the status of the recipient microorganism, and features of the host that promote the progression of disease. The incorporation of certain genes, such as those encoding cholera toxin, would be sufficient to convert any organism into a pathogen because administration of the toxin itself is sufficient to produce the symptoms of the disease. But for most other cases, the utility of sequences obtained through gene transfer varies with the organism. E. coli is a benign constituent of the mammalian intestinal flora and is apparently predisposed to become a pathogen by the introduction of several types of virulence genes. The LEE island is likely to encode all of the genes necessary to produce attachment and effacement lesions, and the acquisition of this island could probably render any strain of E. coli pathogenic. And, not surprisingly, pathogenicity islands causing these lesions have been detected in genetically diversed strains of E. coli.The acquisition of pathogenicity islands offers a rapid method of evolving novel functions; however, the introgressed sequences, even when they encode their specific regulators as part of complete functional units, must interact with rest of the genome. Expression of six invasion genes within the SPI-1 island of Salmonella is governed by the PhoP/PhoQ regulatory system (Galan 1996xGalan, J.E. Mol. Microbiol. 1996; 20: 263–272Crossref | PubMed | Scopus (329)See all ReferencesGalan 1996), which is not encoded within the SPI-1 island and is present in both pathogenic and non-pathogenic microorganisms. And even sequences that are maintained on extrachromosomal elements can be regulated by chromosomal loci: the invasion genes on the Shigella virulence plasmid are controlled by the chromosomally-encoded histone-like protein H1.The association of pathogenicity islands with mobile DNA elements suggests that these sequences could be incorporated into a wide variety of bacterial species. However, presence of a pathogenicity island does not assure the transformation of an organism into a pathogen. A 10 kb region that harbors most known virulence genes in the pathogenic species of Listeria (L. monocytogenes and L. ivanovii) is also present in the chromosome of the nonpathogenic L. seeligeri (Gouin et al. 1994xGouin, E, Mengaud, J, and Cossart, P. Infect. Immun. 1994; 62: 3550–3553PubMedSee all ReferencesGouin et al. 1994). While this gene cluster also encodes a pleiotropic activator, the attenuated phenotype of L. seeligeri has been ascribed to down regulation of most virulence genes. Furthermore, due to the coevolution between microbes and their hosts, the virulence potential of pathogenicity islands will only manifest in suitable animals and plants.Finally, it has been suggested that the deletion of pathogenicity islands may represent a regulatory mechanism to control expression of virulence genes (Blum et al. 1994xBlum, G, Ott, M, Lischewski, A, Ritter, A, Imrich, H, Tschape, H, and Hacker, J. Infect. Immun. 1994; 62: 606–614PubMedSee all ReferencesBlum et al. 1994). This presupposes that the elimination of pathogenicity islands will circumvent the immune response to the encoded determinants and allow rapid microbial replication by reducing chromosome size. While this is a plausible scenario, both pathogenic and non-pathogenic strains of E. coli contain surface antigens that can promote an immune response, and the growth rates of natural strains of E. coli under lab conditions are not associated with genome size. Therefore, the deletion of pathogenicity islands is probably not a mechanism employed by bacteria to modulate virulence, but simply reflects the intrinsic genetic instability of these sequences.

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield more than two orders of magnitude more sensitivity than traditional PCR cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCR-based community structure profiling methods. We tested the effect of amplicon length and primer pair on estimates of species richness (number of species) and evenness (relative abundance of species) by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1–V2 or V8 regions, using amplicons ranging in length from 352 to 1443 bp. Our results show that both amplicon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities.

Evolutionary Origins of Genomic Repertoires in Bacteria

Explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. In eukaryotes, this diversity is believed to result mainly from gene duplication and loss, but in prokaryotes, lateral gene transfer (LGT) can also contribute substantially to genome contents. To determine the histories of gene inventories, we conducted an exhaustive analysis of gene phylogenies for all gene families in a widely sampled group, the γ-Proteobacteria. We show that, although these bacterial genomes display striking differences in gene repertoires, most gene families having representatives in several species have congruent histories. Other than the few vast multigene families, gene duplication has contributed relatively little to the contents of these genomes; instead, LGT, over time, provides most of the diversity in genomic repertoires. Most such acquired genes are lost, but the majority of those that persist in genomes are transmitted strictly vertically. Although our analyses are limited to the γ-Proteobacteria, these results resolve a long-standing paradox—i.e., the ability to make robust phylogenetic inferences in light of substantial LGT.

Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities

Although bacteria are continually acquired over the lifetime of an individual, the phylogenetic relationships of great ape species is mirrored in the compositions of their gut microbial communities.

Cognate gene clusters govern invasion of host epithelial cells by Salmonella typhimurium and Shigella flexneri

The enteric pathogens Salmonella typhimurium and Shigella flexneri differ in most virulence attributes including infectivity, pathology and host range. We have identified a new assemblage of genes responsible for invasion properties of Salmonella which is remarkably similar in order, arrangement and sequence to the gene cluster controlling the presentation of surface antigens (spa) on the virulence plasmid of Shigella. In Salmonella, this chromosomally encoded complex consists of over 12 genes, mutations in which abolish bacterial entry into epithelial cells. Although these genera use distinct invasion antigens, a non‐invasive spa mutant of Salmonella could be rescued by the corresponding Shigella homolog. While spa promotes equivalent functions in Shigella and Salmonella, this constellation of genes has been acquired independently by each genus and displays motifs used by diverse antigen export systems including those required for flagellar assembly and protein secretion.

Strand asymmetries in DNA evolution

The complementary strands of DNA differ with respect to replication and transcription. Both of these processes are asymmetric and can bias the occurrence of mutations between the strands: during replication, the discontinuous lagging strand undergoes certain errors at higher rates, and transcription overexposes the nontranscribed strand to DNA damage while targeting repair enzymes to the transcribed strand. While biases introduced during replication apparently have little impact on sequence evolution, the effects of transcription are observed in the asymmetric patterns of substitution in bacterial genes and might be influencing genome-wide patterns of base composition.