MicrobiologyBytes

Bacteria are generally distinguished from the cells of fungi, plants, and animals (eukaryotes) not only by their much smaller size but also by the absence of certain subcellular structures such as nuclei, internal organelles, and microtubules. Using state-of-the-art microscopy, this paper shows that microtubules do exist in some bacteria. These bacterial microtubules are built from proteins that are closely related to the microtubule proteins in eukaryotes. Bacterial microtubules are smaller in diameter than their counterparts in eukaryotic cells but have the same basic architecture. This paper proposes that bacterial microtubules represent primordial structures that preceded eukaryotic microtubules evolutionarily. Because bacterial microtubules can be produced and handled in the lab more easily than their eukaryotic counterparts, they may become useful tools for microtubule research and anti-cancer drug screening.

Microtubules in Bacteria: Ancient Tubulins Build a Five-Protofilament Homolog of the Eukaryotic Cytoskeleton. (2011) PLoS Biol 9(12): e1001213. doi:10.1371/journal.pbio.1001213
Microtubules play crucial roles in cytokinesis, transport, and motility, and are therefore superb targets for anti-cancer drugs. All tubulins evolved from a common ancestor they share with the distantly related bacterial cell division protein FtsZ, but while eukaryotic tubulins evolved into highly conserved microtubule-forming heterodimers, bacterial FtsZ presumably continued to function as single homopolymeric protofilaments as it does today. Microtubules have not previously been found in bacteria, and we lack insight into their evolution from the tubulin/FtsZ ancestor. Using electron cryomicroscopy, here we show that the tubulin homologs BtubA and BtubB form microtubules in bacteria and suggest these be referred to as “bacterial microtubules” (bMTs). bMTs share important features with their eukaryotic counterparts, such as straight protofilaments and similar protofilament interactions. bMTs are composed of only five protofilaments, however, instead of the 13 typical in eukaryotes. These and other results suggest that rather than being derived from modern eukaryotic tubulin, BtubA and BtubB arose from early tubulin intermediates that formed small microtubules. Since we show that bacterial microtubules can be produced in abundance in vitro without chaperones, they should be useful tools for tubulin research and drug screening.

Tweet

A new study has created a model of what scientists think the first multicellular cooperation might have looked like, showing that yeast cells – in an environment that requires them to work for their food – grow and reproduce better in multicellular clumps than singly.

Researchers found that cells of brewer’s yeast that clumped together were able more effectively to manipulate and absorb sugars in their environment than were similar cells that lived singly. The experiments showed that in environments where the yeast’s sugar food source is dilute and the number of cells is small, the ability to clump together allowed cells that otherwise would have remained hungry and static to grow and divide.

The work used the yeast Saccharomyces cerevisiae, which is commonly used in brewing and bread-making and has long been used by scientists as a model organism for understanding single-celled life. The researchers devised a series of experiments that presented two problems for the yeast cells to solve if they were to take in enough food to grow and divide: the first was how to change their food from an unusable form to a usable form; the second was how to actually take in this food. The researchers put the yeast in a solution of sucrose – table sugar – which is composed of two simpler sugars, glucose and fructose. Yeast lives on sugar, but the sucrose can’t get through the membrane that surrounds the cell. So the yeast makes an enzyme called invertase to chop the sucrose into glucose and fructose, each of which can enter the cell using gate-keeping molecules, called transporters, that form part of the membrane.

Working alone, a single yeast cell in a dilute solution of sucrose would never take in enough glucose and fructose to be able to grow and divide. But by cooperating, clumps of yeast in that same solution might have a chance. With several cells in proximity, all releasing invertase to create smaller sugars, these cooperating yeast cells would increase the density of those sugars near the clump, increasing the chances that each cell could take in enough to grow and divide. Sure enough, when the researchers tested these hypotheses on two strains of yeast, they found that the strain which clumped cells together was growing and dividing, while the yeast cells living alone were not.

Sucrose Utilization in Budding Yeast as a Model for the Origin of Undifferentiated Multicellularity. (2011) PLoS Biol 9(8): e1001122. doi:10.1371/journal.pbio.1001122
We use the budding yeast, Saccharomyces cerevisiae, to investigate one model for the initial emergence of multicellularity: the formation of multicellular aggregates as a result of incomplete cell separation. We combine simulations with experiments to show how the use of secreted public goods favors the formation of multicellular aggregates. Yeast cells can cooperate by secreting invertase, an enzyme that digests sucrose into monosaccharides, and many wild isolates are multicellular because cell walls remain attached to each other after the cells divide. We manipulate invertase secretion and cell attachment, and show that multicellular clumps have two advantages over single cells: they grow under conditions where single cells cannot and they compete better against cheaters, cells that do not make invertase. We propose that the prior use of public goods led to selection for the incomplete cell separation that first produced multicellularity.

Tweet

Recent studies have unearthed a treasure trove of prehistoric virus ‘fossils’, viral genomes or genome segments frozen millions of years ago as integrated copies in the genomes of diverse animal hosts. The fact that these integrated viral fossils can be easily recognized as belonging to modern virus families is stunning given the fact that modern exogenous viruses have replicated and evolved for many millions of years since these viral fossils were captured. Despite high rates of mutation, the evolution of virus sequence is clearly constrained. This constraint comes partially from intrinsic selective forces that limit virus evolution, such as selection for modulation of pathogenicity to the host and the structural constraints of the virus itself. Other major constraints on virus evolution come from the diverse immune strategies imposed by hosts. Cumulatively, these constraints act together to limit all aspects of virus evolution from the swarm of variants produced in a single host to the evolution of expanded host range. These newly identified fossils indicate that constraint on virus evolution might be far greater than has previously been appreciated.

Two-stepping through time: mammals and viruses. (2011) Trends Microbiol. 19(6): 286-294
Recent studies have identified ancient virus genomes preserved as fossils within diverse animal genomes. These fossils have led to the revelation that a broad range of mammalian virus families are older and more ubiquitous than previously appreciated. Long-term interactions between viruses and their hosts often develop into genetic arms races where both parties continually jockey for evolutionary dominance. It is difficult to imagine how mammalian hosts have kept pace in the evolutionary race against rapidly evolving viruses over large expanses of time, given their much slower evolutionary rates. However, recent data has begun to reveal the evolutionary strategy of slowly-evolving hosts. We review these data and suggest a modified arms race model where the evolutionary possibilities of viruses are relatively constrained. Such a model could allow more accurate forecasting of virus evolution.

Tweet

Biologists have uncovered virus fragments from the same family of the modern Hepatitis B virus locked inside the genomes of songbirds such as the modern-day zebra finch. This article marks the first time that endogenous hepadnaviruses have been found in any organism. An endogenous virus is one that deposits itself or fragments of itself into the chromosome of an organism, allowing it to be passed from generation-to-generation. Previously, most of these known “fossilized” virus sequences have come from retroviruses. These fragments have been sitting in the bird’s genomes for at least 19 million years, far longer than anyone previously thought this family of viruses had been in existence.

The researchers dated the hepadnavirus fragments by locating them in the same spot on the genome of five species of passerine birds and then tracing those species to a common ancestor that lived more than 19 million years ago. This work provides a glimpse into an ancient viral world that we never knew existed. The results are remarkable – hepadnaviruses, and likely many other viruses as well, are far older than we previously thought. Another surprise is that the older versions of the hepadnaviruses are remarkably similar to today’s viruses. This suggests that the slow evolution of the hepadnaviruses observed in birds indicates that the viruses are, in the long run, better adapted to their hosts than what is suggested by study of the disease-causing Hepatitis B viruses. Genomic fossils like these remarkable hepadnaviral fossils have the prospect of completely revising our preconceived notions about the age and evolution of such viruses.

This study also opens new avenues for research that might help predict and prevent human viral pandemics originating in bird species. Given that they were infected in the past, it is legitimate to think that some of these birds may still carry such viruses today. We can use this discovery as a guide to screen targeted groups of bird species for the presence of new circulating Hepatitis B-like viruses.

Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses. (2010) PLoS Biol 8(9): e1000495. doi:10.1371/journal.pbio.1000495
Because most extant viruses mutate rapidly and lack a true fossil record, their deep evolution and long-term substitution rates remain poorly understood. In addition to retroviruses, which rely on chromosomal integration for their replication, many other viruses replicate in the nucleus of their host’s cells and are therefore prone to endogenization, a process that involves integration of viral DNA into the host’s germline genome followed by long-term vertical inheritance. Such endogenous viruses are highly valuable as they provide a molecular fossil record of past viral invasions, which may be used to decipher the origins and long-term evolutionary characteristics of modern pathogenic viruses. Hepadnaviruses (Hepadnaviridae) are a family of small, partially double-stranded DNA viruses that include hepatitis B viruses. Here we report the discovery of endogenous hepadnaviruses in the genome of the zebra finch. We used a combination of cross-species analysis of orthologous insertions, molecular dating, and phylogenetic analyses to demonstrate that hepadnaviruses infiltrated repeatedly the germline genome of passerine birds. We provide evidence that some of the avian hepadnavirus integration events are at least 19 My old, which reveals a much deeper ancestry of Hepadnaviridae than could be inferred based on the coalescence times of modern hepadnaviruses. Furthermore, the remarkable sequence similarity between endogenous and extant avian hepadnaviruses (up to 75% identity) suggests that long-term substitution rates for these viruses are on the order of 10^-8 substitutions per site per year, which is a 1,000-fold slower than short-term rates estimated based on the sequences of circulating hepadnaviruses. Together, these results imply a drastic shift in our understanding of the time scale of hepadnavirus evolution, and suggest that the rapid evolutionary dynamics characterizing modern avian hepadnaviruses do not reflect their mode of evolution on a deep time scale.

Related:

1. Phoenix from the ashes: The 5 million year old virus
2. The Island of Fossil Viruses

Traditional treatment of bacterial infections relies heavily on the use of antibacterial compounds that either kill bacteria (bactericidal) or inhibit their growth (bacteriostatic). Typically, the targets for the main conventional antibiotics are essential cellular processes such as bacterial cell wall biosynthesis, bacterial protein synthesis, and bacterial DNA replication and repair. However, resistance to these drugs arises and spreads very rapidly, even to such an extent that bacteria have been identified that are simultaneously resistant to all available antibiotics. The increasing occurrence of resistant bacteria gradually renders antibiotics ineffective in treating infections and has enormous human and economic consequences worldwide. As a result, the identification of novel drug targets and the development of novel therapeutics constitute an important area of current scientific research. An alternative to killing or inhibiting growth of pathogenic bacteria is the specific attenuation of bacterial virulence, which can be attained by targeting key regulatory systems that mediate the expression of virulence factors. One of the target regulatory systems is quorum sensing (QS), or bacterial cell-to-cell communication. QS is a mechanism of gene regulation in which bacteria coordinate the expression of certain genes in response to the presence or absence of small signal molecules. As the importance of QS in virulence development of pathogenic bacteria became clear, about a decade ago, QS disruption was suggested as a new anti-infective strategy.

Although at this moment it is difficult to accurately estimate the risk of resistance development, this paper argues that scientists need to pay attention to the possibility that it will evolve. Once we have better knowledge of the risk of resistance development to QS disruption, it might be possible to direct further research on QS inhibition preferentially towards strategies that include a lower risk of resistance development.

Can Bacteria Evolve Resistance to Quorum Sensing Disruption? 2010 PLoS Pathog 6(7): e1000989. doi:10.1371/journal.ppat.1000989

Recent research has revealed that some plant viruses, like many animal viruses, have measurably evolving populations. Most of these viruses have single-stranded positive-sense RNA genomes, but a few have single-stranded DNA genomes. The studies show that extant populations of these virus species are only decades to centuries old, and the genera in which they are placed have diverged since agriculture was invented, and spread around the world during the Holocene. We suggest that this is not mere coincidence but evidence that the conditions generated by agriculture during this era have favoured particular viruses. There is also evidence, albeit less certain, that some plant viruses, including a few shown to have measurably evolving populations, have much more ancient origins. We discuss the possible reasons for this clear discordance between short-term and long-term evolutionary rate estimates, and how it might result from a large timescale dependence of the evolutionary rates. We also discuss briefly why it is useful to know the rates of evolution of plant viruses.

Time – the emerging dimension of plant virus studies. J Gen Virol. Nov 4 2009

Related:

• Plant viruses: master explorers of evolutionary space. Curr Opin Genet Dev. 1993 3(6): 873-877
• Experimental evolution of plant RNA viruses. Heredity. 2008 100(5): 478-483
• Resistance to Plant Viruses

New mass sequencing techniques are revealing that the diversity of viruses is much greater than ever imagined. In this article in Microbiology Today (pdf) Peter Simmonds shows that some recent “new” viruses are providing clues to how viruses evolve:

One of the immediate problems facing evolutionary studies of viruses is the evident fact that viruses are hugely diverse in size, appearance, even the nature of their genetic material (DNA or RNA). From this, it is reasonably clear that they are a not a single evolutionary group, and cannot be easily added as a single unit to the tree of life with its three main divisions (Bacteria, Archaea and Eukarya). By the same token, it seems likely that different virus groups (e.g. animal RNA viruses, retroviruses, large DNA viruses, bacteriophages) may indeed have entirely separate evolutionary origins. In this article I will describe two areas where recent discoveries have produced tantalizing new insights into the origin and ubiquity of some of these groups. Through the application of new, mass-sequencing techniques and scope for large-scale environmental sampling for virus genomic sequences, we may finally be able to understand the extent and complexity of the “virosphere” in which we live, and the extraordinary diversity of viruses that infect us.

Read more

Related:

• Evolutionary history and phylogeography of human viruses
• One virus particle can be enough to cause infection
• Coevolution with viruses drives bacterial mutations

Some canyons in Israel have north and south-facing slopes that have completely different environments, despite their close proximity. In this article in Microbiology Today (pdf) Johannes Sikorski looks at the micro-organisms that live in these habitats and come to some surprising conclusions that might help us understand micro-evolution rather better:

Bacteria and archaea are genetically, phylogenetically and physiologically very diverse. But how does such diversity start to evolve? How do the first subtle and tender lineages begin to accrue? Oh, you might say, that’s trivial. Have a look at the textbooks and you will find everything there about the evolutionary interplay of mutation, recombination, natural selection and genetic drift. The theoretical framework of population genetics is extremely well-developed. Even more, you insist, microbial microevolution has and still is being analysed in very elegant laboratory experiments, where microbes are allowed to mutate, adapt and evolve in test tubes under very stringent and therefore reproducible and adjustable conditions. But may I remind you that the majority of bacteria are neither evolving in a computer, nor are they living in the pencils of mathe-maticians and theoretical population geneticists, nor in laboratory test tubes, although all these approaches yield tremendous results. Most bacteria live outside in the environment, in water, soil, rocks, plants, etc. Here, where they face a great plethora of biotic and abiotic challenges, they evolve and speciate. Shouldn’t we look at how evolution happens in nature, even though as passive observers, we researchers cannot control this process? What are the decisive factors? Is it possible to catch a glimpse of such a natural evolutionary experiment?

Read more

Related:

• What is a bacterial species?
• Genomic islands in bacterial evolution
• Evolution of root nodule symbiosis with nitrogen-fixing bacteria

A cockatrice was a flamboyant sight at medieval banquets, featuring a roasted chimera of rooster fused to a suckling pig. In this article in Microbiology Today (pdf) Ed Bolt and Stephane Delmas suggest that there are similarities with archaea, ancient micro-organisms that have features of both bacteria and eukaryotes within their genomes:

Archaea and bacteria are micro-organisms that are similar, yet different. Archaea are evolutionarily ancient organisms that have soaked up diverse ecosystems for at least 2.5 billion years. They are, like bacteria, unencumbered by various complex sub-cellular structures (e.g. mitochondria, a membrane-bound nucleus) and as such have been for most of their long existence, or at least from when microbiologists started looking at them, considered to be bacteria that had evolved to thrive in extreme environments (e.g. at high temperature or salinity). For this reason they were often called archeabacteria. However, DNA sequencing experiments in the 1970s drove a wedge through the bacteria, splitting it into two separate domains of cellular life: the Bacteria and the Archaea. The genetic distinction between bacteria and archaea is now generally accepted since its original proposal in 1977, but has its evolutionary root much earlier, probably pre-dating the emergence of oxygen 2.5 billion years ago. Therefore, the classification of cellular organisms is now usually represented in a tree of life consisting of three domains, Bacteria, Archaea and Eukarya.

Read more

Related:

• Unique cell division machinery in the Archaea