MicrobiologyBytes

MicrobiologyBytes is taking a well earned rest for a week or so but we’ll be back in January. In the meantime:

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.

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It was my privilege to work with Phil Minor during my PhD. 25 years later (gulp), Phil looks back and forward to the polio endgame.

The Polio-Eradication programme and issues of the end game. J Gen Virol. Nov 29 2011
Poliovirus causes paralytic poliomyelitis, an ancient disease of humans that became a major public health issue in the 20th century. The primary site of infection is the gut where virus replication is entirely harmless; the two very effective vaccines developed in the 1950s (Oral Polio Vaccine, or OPV and Inactivated Polio Vaccine, or IPV) induce humoral immunity which prevents viraemic spread and disease. The success of vaccination in developing countries and in middle income countries encouraged the World Health Organization to commit itself to an eradication programme which has made great advances. The features of the infection including its largely silent nature and the ability of the live vaccine (OPV) to evolve and change in vaccine recipients and their contacts make eradication particularly challenging. Understanding the pathogenesis and virology of the infections is of major significance as the programme reaches its conclusion.

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The delightful NCBI ROFL carried this item recently. Certainly something to think about over the “festive” season.

Scent Recognition of Infected Status in Humans. J Sex Med. Dec 6 2011. doi: 10.1111/j.1743-6109.2011.02562.x
There is a body of experimental evidence that mice and rats use chemical signals to avoid sexual contact with infected conspecifics. In contrast to animals, body scent of sick humans is employed only in medical diagnostics. A modification of human body odor, due to an infection, has not been studied as a potential signal for choice of a sexual partner. It might, however, be especially important for sexually transmitted infections (STI) because many such infections have no obvious external manifestations.
Aim: In this study, we have investigated odor pleasantness of young men infected with gonorrhea, Neisseria gonorrhoeae.
Methods:We collected armpit sweat and saliva from young men (17-25 years old) belonging to three groups: healthy persons (N=16), young men infected with gonorrhea, Neisseria gonorrhoeae (N=13), and persons recovered due to specific therapy (N=5). The sweat samples odor was then assessed by healthy young women (17-20 years old). Concentrations of cortisol, testosterone, immunoglobulin A (IgA), and immunoglobulin G (IgG) were measured in saliva by means of enzyme-linked immunosorbent assay.
Main Outcome Measures: Subjective rates of odor pleasantness, association of scent of armpit sweat with odor descriptors, stepwise regression of odor pleasantness and salivary cortisol, testosterone, IgA, and IgG. Results: The odor from infected individuals was reported as less pleasant in comparison with the odor of healthy and recovered young men. The scent of infected men was more frequently associated by raters with the descriptor “putrid.” Odor pleasantness of the male sweat correlated negatively with concentration of the nonspecific salivary IgA and IgG, which was measured as an indicator of current immunoenhancement.
Conclusion: Perhaps, the immune-dependent reduction of the scent pleasantness in the acute phase of STI is part of an evolutionary mechanism ensuring, unconsciously, avoidance of a risky romantic partner.

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Although it has not been in the news much recently, the highly pathogenic avian influenza A virus subtype H5N1 has been endemic in some bird species since its emergence in 1996 and its ecology, genetics and antigenic properties continue to evolve. This has allowed diverse virus strains to emerge in endemic areas with altered receptor specificity, including a new H5 sublineage with enhanced binding affinity to the human-type receptor. The pandemic potential of H5N1 viruses is alarming and may be increasing. This article reviews the complex and changing nature of the H5N1 virus that may contribute to the emergence of pandemic strains – with really serious consequences.

The changing nature of avian influenza A virus (H5N1). Tresnd in Microbiology, 5 December 2011

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During the past decade, there has been a striking increase in Clostridium difficile infections worldwide predominantly due to the emergence of epidemic or hypervirulent isolates, leading to an increased research focus on this bacterium. Particular interest has surrounded the two large clostridial toxins encoded by most virulent isolates, known as toxin A and toxin B. Toxin A was thought to be the major virulence factor for many years; however, it is becoming increasingly evident that toxin B plays a much more important role than anticipated. It is clear that further experiments are required to accurately determine the relative roles of each toxin in disease, especially in more clinically relevant current epidemic isolates.

The role of toxin A and toxin B in the virulence of Clostridium difficile. Trends in Microbiology, 7 December 2011

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When HIV infects a T lymphocyte, it first inserts a copy of its genome into the cell’s DNA. This inserted virus, called a provirus, then races to make as many new viruses as possible before its host cell dies. But in a few infected cells, HIV does not immediately turn its host into a viral factory. Instead, the provirus is carried around in the DNA of the cell as a transcriptionally silent (“latent”) passenger, only to explode back into action at a later time, when its host cell attempts to participate in an immune response to infection by other pathogens. Because they target the products of HIV transcription, current antiviral therapies like HAART can’t kill latent HIV. And because a full-blown infection can be re-established from a tiny reservoir of latently infected cells, viral latency is an important contributor to our struggle against HIV (Dissecting HIV’s Latent Menace. (2011) PLoS Biol 9(11): e1001209).

The following article examines the molecular mechanism responsible for the establishment and maintenance of HIV latency and its re-activation, and uncovers the role played in this process by the SWI/SNF class of chromatin remodeling complexes, which use energy from ATP to alter the structure of chromatin. Two distinct sub-classes of SWI/SNF, BAF and PBAF, play functionally opposing roles in distinct steps of the HIV promoter (or long terminal repeat, LTR) transcription cycle. The PBAF complex augments transcription of the LTR by the viral transactivator Tat. In contrast, the distinct BAF complex generates a chromatin structure at the LTR that is energetically unfavorable with respect to the intrinsic histone-DNA sequence preferences. Specifically, BAF positions a repressive nucleosome immediately downstream of the HIV transcription start site, abrogating transcription, and in this way contributes to the establishment and maintenance of HIV latency. The data describe a novel molecular mechanism for the establishment and maintenance of HIV latency, and we identify the catalytic subunit of BAF, the enzyme BRG1, as a putative molecular target to deplete the latent reservoir in infected patients.

Repressive LTR Nucleosome Positioning by the BAF Complex Is Required for HIV Latency. (2011) PLoS Biol 9(11): e1001206
Persistence of a reservoir of latently infected memory T cells provides a barrier to HIV eradication in treated patients. Several reports have implicated the involvement of SWI/SNF chromatin remodeling complexes in restricting early steps in HIV infection, in coupling the processes of integration and remodeling, and in promoter/LTR transcription activation and repression. However, the mechanism behind the seemingly contradictory involvement of SWI/SNF in the HIV life cycle remains unclear. Here we addressed the role of SWI/SNF in regulation of the latent HIV LTR before and after transcriptional activation. We determined the predicted nucleosome affinity of the LTR sequence and found a striking reverse correlation when compared to the strictly positioned in vivo LTR nucleosomal structure; sequences encompassing the DNase hypersensitive regions displayed the highest nucleosome affinity, while the strictly positioned nucleosomes displayed lower affinity for nucleosome formation. To examine the mechanism behind this reverse correlation, we used a combinatorial approach to determine DNA accessibility, histone occupancy, and the unique recruitment and requirement of BAF and PBAF, two functionally distinct subclasses of SWI/SNF at the LTR of HIV-infected cells before and after activation. We find that establishment and maintenance of HIV latency requires BAF, which removes a preferred nucleosome from DHS1 to position the repressive nucleosome-1 over energetically sub-optimal sequences. Depletion of BAF resulted in de-repression of HIV latency concomitant with a dramatic alteration in the LTR nucleosome profile as determined by high resolution MNase nucleosomal mapping. Upon activation, BAF was lost from the HIV promoter, while PBAF was selectively recruited by acetylated Tat to facilitate LTR transcription. Thus BAF and PBAF, recruited during different stages of the HIV life cycle, display opposing function on the HIV promoter. Our data point to the ATP-dependent BRG1 component of BAF as a putative therapeutic target to deplete the latent reservoir in patients.

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It has been argued that the smaller viruses associated with giant DNA viruses are a new biological entity. However, a short article in Nature Reviews Microbiology argues that these smaller viruses should be classified with the satellite viruses (which I tend to agree with).

Virophages or satellite viruses? Nature Reviews Microbiology 9, 762-763 (November 2011) | doi:10.1038/nrmicro2676
Studies on the giant DNA viruses Acanthamoeba polyphaga mimivirus (APMV) and Cafeteria roenbergensis virus (CroV) have revealed that much smaller viruses – Sputnik and Mavirus, respectively – are associated with them. These smaller viruses depend on the giant viruses for propagation, although the giant viruses can grow without the smaller viruses. It has been argued that Sputnik represents a new, previously unknown biological entity: a ‘virophage’. This term is now used by an increasing number of researchers. However, the virophage concept and its status as a new biological entity requires objective assessment of the similarities and differences between the virophages and the ‘classical’ satellite viruses that have been described previously.

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Prematurity is the leading cause of neonatal deaths and long-term infant disability, with the rate of preterm births continuing to rise. Despite improved medical and respiratory management, the mortality rate for the most premature infants remains high. Extremely low birth weight infants are at increased risk for complications such as sepsis, meningitis, necrotizing enterocolitis and poor growth- problems, all associated with high risk for neurodevelopmental impairment, and all of which may be impacted by the microbial communities in their gut. Among premature infants, frequently used treatments, such as antibiotics and histamine-2 blockers are associated with an increased risk of necrotizing enterocolitis and may exert their influence via alternations in gut microbiota.

This paper uses molecular methods to resolve the microbial constituents of the gut-associated microbiome in premature babies. The study highlights unprecedented early fungal diversity, evidence of roundworms, human and bacterial viruses, and a bacterial community harboring many potential pathogens.

Beyond Bacteria: A Study of the Enteric Microbial Consortium in Extremely Low Birth Weight Infants. (2011) PLoS ONE 6(12): e27858
Extremely low birth weight (ELBW) infants have high morbidity and mortality, frequently due to invasive infections from bacteria, fungi, and viruses. The microbial communities present in the gastrointestinal tracts of preterm infants may serve as a reservoir for invasive organisms and remain poorly characterized. We used deep pyrosequencing to examine the gut-associated microbiome of 11 ELBW infants in the first postnatal month, with a first time determination of the eukaryote microbiota such as fungi and nematodes, including bacteria and viruses that have not been previously described. Among the fungi observed, Candida sp. and Clavispora sp. dominated the sequences, but a range of environmental molds were also observed. Surprisingly, seventy-one percent of the infant fecal samples tested contained ribosomal sequences corresponding to the parasitic organism Trichinella. Ribosomal DNA sequences for the roundworm symbiont Xenorhabdus accompanied these sequences in the infant with the greatest proportion of Trichinella sequences. When examining ribosomal DNA sequences in aggregate, Enterobacteriales, Pseudomonas, Staphylococcus, and Enterococcus were the most abundant bacterial taxa in a low diversity bacterial community (mean Shannon-Weaver Index of 1.02±0.69), with relatively little change within individual infants through time. To supplement the ribosomal sequence data, shotgun sequencing was performed on DNA from multiple displacement amplification (MDA) of total fecal genomic DNA from two infants. In addition to the organisms mentioned previously, the metagenome also revealed sequences for gram positive and gram negative bacteriophages, as well as human adenovirus C. Together, these data reveal surprising eukaryotic and viral microbial diversity in ELBW enteric microbiota dominated bytypes of bacteria known to cause invasive disease in these infants.

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