Glutamine synthetase gene evolution in bacteria

The evolution of the prokaryotic glutamine synthase (GS) genes, namely the GSI and GSII isoforms, has been investigated using the second codon positions, which have previously proven to behave as a good molecular clock. Our data confirm the early divergence between prokaryotic and eukaryotic GSII before the splitting between plants and animals. The phylogenetic tree of the GSI isoforms shows Archaebacteria to be more closely related to Eubacteria than to Eukaryotes. This finding is confirmed by the phylogenetic analysis carried out on both large and small subunits of rRNA. However, differently from the rRNA analyses, Crenarchaeota and Euryarchaeota Archaebacteria, as well as high- and low-GC gram-positive bacteria, appear to be polyphyletic. We provide evidence that the observed polyphyly of Archaebacteria might be only apparent, resulting from a gene duplication event preceding the split between Archaebacteria and Eubacteria and followed by the retention of only one isoform in the extant lineages. Both gram-negative bacteria and high-GC gram-positive bacteria, which appear closely related, have GS activity regulated by an adenylylation/deadenylylation mechanism. A lateral gene transfer from Archaebacteria to low-GC eubacteria is invoked to explain the observed polyphyly of gram-positive bacteria.      

Bacterial resistance evolution by recruitment of super-integron gene cassettes

The capture and spread of antibiotic resistance determinants by integrons underlies the rapid evolution of multiple antibiotic resistance among diverse Gram-negative clinical isolates. The association of multiple resistance integrons (MRIs) with mobile DNA elements facilitates their transit across phylogenetic boundaries and augments the potential impact of integrons on bacterial evolution. Recently, ancestral chromosomal versions, the super-integrons (SIs), were found to be genuine components of the genomes of diverse bacterial species. SIs possess evolutionary characteristics and stockpiles of adaptive functions, including cassettes related to antibiotic resistance determinants previously characterized in clinical isolates, which suggest that MRIs and their resistance genes were originally recruited from SIs and their pool of amassed genes. However, the recombination activity of integrons has never been demonstrated in a bacterium other than Escherichia coli. We introduced a naturally occurring MRI (TpR, SulR) on a conjugative plasmid into Vibrio cholerae, a species known to harbour a SI. We show that MRIs can randomly recruit genes directly from the cache of SI cassettes. By applying a selective constraint for the development of antibiotic resistance, we demonstrate bacterial resistance evolution through the recruitment a novel, but phenotypically silent, chloramphenicol acetyltransferase gene from the V. cholerae SI and its precise insertion into the MRI. The resulting resistance profile (CmR, TpR, SulR) could then be disseminated by conjugation to other clinically relevant pathogens at high frequency. These results demonstrate that otherwise phenotypically sensitive strains may still be a genetic source for the evolution of resistance to clinically relevant antibiotics through integron-mediated recombination events.     

Bacterial evolution

The deliberate application of the methodology of contemporary molecular genetics to problems in bacterial systematics has led to a broad new understanding of the evolutionary history of both prokaryotes and eukaryotes. In this review, I discuss some of the major conclusions of this endeavour and try to predict future directions.     

Bacterial pathogen evolution: breaking news

The immense social and economic impact of bacterial pathogens, from drug-resistant infections in hospitals to the devastation of agricultural resources, has resulted in major investment to understand the causes and consequences of pathogen evolution. Recent genome sequencing projects have provided insight into the evolution of bacterial genome structures; revealing the impact of mobile DNA on genome restructuring and pathogenicity. Sequencing of multiple genomes of related strains has enabled the delineation of pathogen evolution and facilitated the tracking of bacterial pathogens globally. Other recent theoretical and empirical studies have shown that pathogen evolution is significantly influenced by ecological factors, such as the distribution of hosts within the environment and the effects of co-infection. We suggest that the time is ripe for experimentalists to use genomics in conjunction with evolutionary ecology experiments to further understanding of how bacterial pathogens evolve.     

Bacterial genomes: evolution of pathogenicity

Bacterial pathogens continue to pose a major threat to economically important plant resources. Disease outbreaks can occur through rapid evolution of a pathogen to overcome host defences. The advent of genome sequencing, especially next-generation technologies, has seen a revolution in the study of plant pathogen evolution over the past five years. This review highlights recent developments in understanding bacterial plant pathogen evolution, enabled by genomics and specifically focusing on type III protein effectors. The genotypic changes and mechanisms involved in pathogen evolution are now much better understood. However, there is still much to be learned about the drivers of pathogen evolution, both in terms of plant resistance and bacterial lifestyle.     

Bacterial evolution: Jittery genomes.

Recent studies of long-term experimental populations of bacteria have revealed the actual progression of evolutionary change and how rates of phenotypic evolution can be decoupled from rates of genomic evolution.     

Molecular evolution of the actin-like MreB protein gene family in wall-less bacteria

The mreB gene family encodes actin-like proteins that determine cell shape by directing cell wall synthesis and often exists in one to three copies in the genomes of non-spherical bacteria. Intriguingly, while most wall-less bacteria do not have this gene, five to seven mreB homologs are found in Spiroplasma and Haloplasma, which are both characterized by cell contractility. To investigate the molecular evolution of this gene family in wall-less bacteria, we sampled the available genome sequences from these two genera and other related lineages for comparative analysis. The gene phylogenies indicated that the mreB homologs in Haloplasma are more closely related to those in Firmicutes, whereas those in Spiroplasma form a separate clade. This finding suggests that the gene family expansions in these two lineages are the results of independent ancient duplications. Moreover, the Spiroplasma mreB homologs can be classified into five clades, of which the genomic positions are largely conserved. The inference of gene gains and losses suggests that there has been an overall trend to retain only one homolog from each of the five mreB clades in the evolutionary history of Spiroplasma.     

Bacterial evolution: chromosome arithmetic and geometry

Recent sequencing projects have characterized bacterial genomes that are organized onto elements of various sizes, shapes and numbers. Aside from its biological relevance and curiosity, this diversity calls into question the way that we define bacterial chromosomes.     

Bacterial evolution and metabolism

This article examines the relationship between (or dependence of) bacterial evolution in prokaryotes and metabolism, and the changing physical-chemical conditions present during early evolution.     

Bacterial evolution and silicon

This review examines the possible role of silicon in molecular evolution. It is possible silicon participated in early molecular evolution by providing a stable mineral surface or gel structure where the assembly and replication of primitive genetic information occurred. However, as molecular evolution proceeded, silicon was not required in the evolution of C-based organisms. Silicon can be accumulated by diatoms and other living organisms such as silicoflagellates, some xanthophytes, radiolarians and actinopods and plants such as grasses, ferns, horseradish, some trees and flowers, some sponges, insects and invertebrates and bacteria and fungi. Silicon also has a role in synthesis of DNA, DNA polymerase and thymidylate kinase activity in diatoms. It is not unreasonable to examine the role of silicon in early molecular evolution as it may have been part of a micro-environment in which assembly of genetic information occurred.     

A microbiologist's odyssey: Bacterial viruses to photosynthetic bacteria

Perspective can be defined as the relationships or relative importance of facts or matters from any special point of view. Thus, my Personal perspective reflects the threads I followed in a 50-year journey of research in the complex tapestry of bioenergetics and various aspects of microbial metabolism. An early interest in biochemical and microbial evolution led to the fertile hunting grounds of anoxygenic photosynthetic bacteria. Viewed as a physiological class, these organisms show remarkable metabolic versatility in that certain individual species are capable of using all the known major types of energy conversion (photosynthetic, respiratory, and fermentative) to support growth. Since such anoxyphototrophs are readily amenable to molecular genetic/biological manipulation, it can be expected that they will eventually provide important clues for unraveling the evolutionary relationships of the several kinds of energy conversion. I gradually came to believe that understanding the evolution of phototrophs would require detailed knowledge not only of how light is converted to chemical energy, but also of a) pathways of monomer production from extracellular sources of carbon and nitrogen and b) mechanisms cells use for integrating ATP regeneration with the energy-requiring biosyntheses of biological macromolecules. Serendipic observation of photoproduction of H₂ from organic compounds by Rhodospirillum rubrum in 1949 led to discovery of N₂ fixation by anoxyphototrophs, and this capacity was later exploited for the isolation of hitherto unknown species of photosynthetic prokaryotes, including the heliobacteria. Recent studies on the reaction centers of the heliobacteria suggest the possibility that these bacteria are descendents of early phototrophs that gave rise to oxygenic photosynthetic organisms.Abbreviations AMP adenosine monophosphate - ADP adenosine diphosphate - ATP adenosine triphosphate - ATPase adenosine triphosphatase - Bchl bacteriochlorophyll - DMSO dimethyl sulfoxide - NADH reduced nicotinamide adenine dinucleotide - nif ^– genes for dinitrogen fixation - Nif^– bacterial mutants incapable of dinitrogen fixation - O/R oxidation/reduction - P_i inorganic orthophosphate - R. capsulatus Rhodobacter capsulatus - R. sphaeroides Rhodobacter sphaeroides - Rps. Rhodopseudomonas - TMAO trimethyl amine-N-oxide Written at the invitation of Govindjee.     

Bacterial genomics and pathogen evolution

The availability of hundreds of bacterial genome sequences has altered the study of bacterial pathogenesis, affecting both design of experiments and analysis of results. Comparative genomics and genomic tools have been used to identify virulence factors and genes involved in environmental persistence of pathogens. However, a major stumbling block in the genomics revolution has been the large number of genes with unknown function that have been identified in every organism sequenced to date.     

The mechanisms of horizontal gene transfer: the role of bacteriophages and integrons in the evolution of pathogenic bacteria

The role of bacteriophages, e.g. filamentous phages, whose single-stranded DNA comprise the coding virulence factors, as well as of certain suspected bacteriophage derivatives like constin-elements, integrons and chromosomal super-integron, played by them in the horizontal gene transfer and in the evolution of bacteria is under discussion.     

Bacterial evolution of antibiotic hypersensitivity

The evolution of resistance to a single antibiotic is frequently accompanied by increased resistance to multiple other antimicrobial agents. In sharp contrast, very little is known about the frequency and mechanisms underlying collateral sensitivity. In this case, genetic adaptation under antibiotic stress yields enhanced sensitivity to other antibiotics. Using large‐scale laboratory evolutionary experiments with Escherichia coli, we demonstrate that collateral sensitivity occurs frequently during the evolution of antibiotic resistance. Specifically, populations adapted to aminoglycosides have an especially low fitness in the presence of several other antibiotics. Whole‐genome sequencing of laboratory‐evolved strains revealed multiple mechanisms underlying aminoglycoside resistance, including a reduction in the proton‐motive force (PMF) across the inner membrane. We propose that as a side effect, these mutations diminish the activity of PMF‐dependent major efflux pumps (including the AcrAB transporter), leading to hypersensitivity to several other antibiotics. More generally, our work offers an insight into the mechanisms that drive the evolution of negative trade‐offs under antibiotic selection.     

Molecular evolution in bacteria

Recent advances in microbiology and molecular biology have a unifying influence on our understanding of genetic diversity/similarity and evolutionary relationships in microorganisms. This article attempts to unify information from diverse areas such as microbiology, molecular biology, microbial physiology, clay crystal genes, metals-microbe-clay interactions and bacterial DNA restriction-modification systems (R-M) as they may apply to molecular evolution of bacteria. The possibility is discussed that the first informational molecules may have been catalytic RNA (micro-assembler) not DNA (now the master copy) and these first micro-assemblers may have been precursors of ribosomes.