MicrobiologyBytes

The advent of genetic engineering – the ability to edit and insert DNA into living organisms – in the latter half of the 20th century created visions of a new era of synthetic biology, where novel biological functions could be designed and implemented for useful purposes. We are witnessing an exciting revolution of scale, wherein technical progresses allow for the manipulation of genetic material at the whole genome level. This will enable the manufacture of increasingly complex genetic designs to solve pressing challenges in health, energy and the environment-if and when such designs can be specified.

This paper argues that the organized development of key common application organisms, engineered for engineerability, and attendant libraries of parts, pathways and standardized manufacturing are necessary for this genome-scale technology to realize its promise.

Toward rational design of bacterial genomes. Curr Opin Microbiol. Aug 22 2011

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Before the genomic era there was already a longstanding interest in understanding the origins of bacterial pathogens and the molecular attributes of virulence. Large-scale genome sequencing has provided a rapid and unbiased means of uncovering the evolution of many pathogens, contributing to both fundamental microbiological insights and the development of new disease-control strategies. For these reasons, the evolution of one of the most devastating human pathogens, Mycobacterium tuberculosis, has captivated researchers since its discovery in 1882. This interest was stimulated not only by the epidemiologic importance of the pathogen but also by the lack of consensus on its origins and its apparent exception to the stereotypes of bacterial evolution (e.g. acquisition of pathogenicity islands). So where did M. tuberculosis come from?

The rise and fall of the Mycobacterium tuberculosis genome. Trends Microbiol. 2011 19(4): 156-161
When studied from the perspective of non-tuberculous mycobacteria (NTM) it is apparent that Mycobacterium tuberculosis has undergone a biphasic evolutionary process involving genome expansion (gene acquisition and duplication) and reductive evolution (deletions). This scheme can instruct descriptive and experimental studies that determine the importance of ancestral events (including horizontal gene transfer) in shaping the present-day pathogen. For example, heterologous complementation in an NTM can test the functional importance of M. tuberculosis-specific genetic insertions. An appreciation of both phases of M. tuberculosis evolution is expected to improve our fundamental understanding of its pathogenicity and facilitate the evaluation of novel diagnostics and vaccines.

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Influenza A virus is the prototype of the Orthomyxoviridae, and like all members of this family, the negative-sense RNA that comprises its genome is divided into separate segments. These vRNA segments share a common organisation; a long central coding region (in antisense), sometimes encoding more than one polypeptide, flanked by relatively short untranslated regions (UTRs) and at the termini, sequences conserved between segments that show partial complementarity. The vRNA segments are separately encapsidated into ribonucleoprotein (RNP) structures by viral polypeptides. These RNPs act as independent units for the purposes of viral RNA synthesis, which occurs in the nuclei of infected cells. Replicated vRNAs are exported (as RNPs) from the nucleus via the cellular CRM1 pathway, and at the final stage of viral assembly, are incorporated into the virion as it buds from the apical plasma membrane of the cell. The process of virion assembly is not well understood but is thought to involve a series of protein-protein interactions between the cytoplasmic tails of the viral integral membrane proteins, the matrix protein and the RNPs.

Genome segmentation confers evolutionary advantages on influenza viruses, but also poses a problem in virion assembly. The eight segments encode 12 identified polypeptides. At least one copy of each of the eight vRNAs must be packaged for a single virion to be able to initiate a productive infection. Until recently, the process by which this was achieved was poorly understood, but a clearer picture has begun to emerge of a mechanism for specifically packaging a full genome, mediated by cis-acting packaging signals in the vRNAs. This review aims to summarise the thought processes and experimental evidence leading up to the currently accepted model for influenza A genome packaging and to highlight the main questions remaining.

Genome packaging in influenza A virus. J Gen Virol. Dec 2 2009

Related:

• Animation of influenza replication
• The Biology of Influenza
• Hungry for hosts – gene flow in influenza virus

Human disease attributable to variola virus (VARV), the etiologic agent of smallpox, has been reported in human populations for more than 2,000 years. VARV is unique among orthopoxviruses in that it is an exclusively human pathogen. Because it has a large, slowly evolving DNA genome, researchers were able to construct a phylogeny of VARV by analyzing single nucleotide polymorphisms (SNPs) from genome sequences of 47 VARV isolates with broad geographic distributions. The results reveal two primary VARV clades, which are likely to have diverged from an ancestral African rodent-borne variola-like virus either 16,000 or 68,000 years before present (YBP), depending on which historical records (East Asian or African) are used to calibrate the molecular clock. One primary clade was represented by the Asian VARV major strains, the more clinically severe form of smallpox, which spread from Asia either 400 or 1,600 YBP. The other primary clade included both alastrim minor, a phenotypically mild smallpox described from the Americas, and isolates from West Africa. This clade diverged from an ancestral VARV either 1,400 or 6,300 YBP.
Observations of smallpox-typical skin rashes on Egyptian mummies dating from 1100 to 1580 B.C. gave credibility to theories that ancient Egypt was an early (and perhaps the earliest) smallpox endemic region. However, smallpox researchers noted that “The most striking thing about smallpox is its absence from the books of the Old and New Testaments, and also from the literature of the Greeks and Romans. Such a serious disease as variola major is very unlikely to have escaped a description by Hippocrates if it existed.” Historical records from Asia describe evidence of smallpox-like disease in medical writings from ancient China (1122 B.C.) and India (as early as 1500 B.C.). The earliest unmistakable description of smallpox first appears in the 4th century A.D. in China, the 7th century A.D. in India and the Mediterranean, and the 10th century A.D. in southwestern Asia. These early Asian descriptions could indicate that pandemic smallpox originated in East Asia. Sequence analysis indicates that divergence between VARV and rodent poxviruses occurred from 16,000 YBP to 68,000 YBP, and that VARV seems to have evolved from a pathogen of African rodents and subsequently spread out of Africa.
On the origin of smallpox: Correlating variola phylogenics with historical smallpox records
PNAS USA 2007 104:15787-15792

What does this all mean?

• In spite of concerns about bioterrorism, smallpox is no longer a major human pathogen, but understanding the origin of this disease, which has been of major importance for most of human history, offers glimpses into how we might rapidly understand new emerging diseases as they appear.
• For a long time it has been generally believed the the most probable origin for smallpox virus was in Asia, but as with yellow fever and HIV, this new research seems to show that smallpox originally came out of Africa.

Update: The end of the world? Dr Franken-Venter? Nope

Craig Venter has built a synthetic genome out of laboratory chemicals and is poised to announce the creation of the first artificial life form. A team of 20 scientists led by Nobel laureate Hamilton Smith has constructed a synthetic chromosome which is 381 genes long and contains 580,000 base pairs of DNA. The nucleotide sequence is based on the bacterium Mycoplasma genitalium which the team pared down to the bare essentials needed to support life, removing a fifth of its genetic make-up. The wholly synthetically reconstructed chromosome, which the team have called Mycoplasma laboratorium, has been tagged with watermarks for easy recognition and transplanted into a living bacterial cell to become a new life form. Venter has further heightened the controversy surrounding his potential breakthrough by applying for a patent for the synthetic bacterium.

Good idea, or not?