Milestones in Microbiology Over the Last 7 Decades

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* 1950’s – Transduction is described for the first time

In 1952 Lederberg and Zinder demonstrated that viruses are able to transfer genetic material from one bacterial strain to another via a process now known as transduction (1). These viruses, known as phage, are able to enter a bacterial cell, integrate themselves into the host cell’s genome, and effectively hijack the host’s genetic machinery to replicate its genetic material alongside the cell’s own DNA. The phage are then able to extricate themselves from the host genome, however, the process is not perfect. Genetic material is often left behind (which may be from a previous bacterial host) or extra taken with it. By this process, phage are able to traffic genes between bacterial strains and species. Lederberg and Zinder demonstrated the phenomenon in Salmonella typhimurium, but over the decades transduction has been demonstrated to be widespread through bacterial populations and an important mechanism in the spread of antimicrobial resistance genes.

* 1960’s – Understanding the basis of control

In 1960, Jacob, Perrin, Sanchez and Monod proposed that groups of bacterial genes may be controlled together in what they dubbed an operon (2). They described a group of genes whose transcription is governed by an operator gene encoded with them. They found that operator activity is governed by an intermediary repressor, the production of which is in turn controlled by a regulator, not necessarily encoded near the operon group. The operon they were describing is now known as the lac operon, responsible for lactose metabolism, but the principle underlies the fundamental structure of many gene groups across a plethora of bacterial species. Their observations went a long way towards understanding observations made about lactose metabolism in E. coli and would go on to earn Jacob and Monod, along with fellow molecular biologist Lwoff, the Nobel Prize for Medicine or Physiology in 1965. Elucidation of the operon was an important step forward in understanding the way in which bacterial genes are regulated. The process has subsequently been exploited by many researchers to artificially overexpress proteins of interest in a controllable manor. The gene of interest is cloned into a plasmid containing a lac repressor and grown in E. coli, from which it can then be purified and used for experimental purposes.

* 1970’s – An end to the smallpox scourge

In 1979, it was declared that smallpox (variola), which killed many and left survivors severely pockmarked, had been officially eliminated. The last natural case was seen in Somalia in 1977. However, small quantities remain held under tight control in the US and former USSR Smallpox vaccination has a long history, but vaccination in earnest is often attributed to starting with Edward Jenner in 1758 (3). However, smallpox continued to kill people across the world for another 200 years prior to a strict vaccination programme implemented by the WHO which commenced in 1959 and intensified in 1966 (4). Smallpox is the only human microbial disease that has ever been eliminated to date.

* 1980’s – One man takes proving his point to the extreme

In 1984, Marshall demonstrated that stomach ulcers can be caused by the bacterium Campylobacter pylori, later called Helicobacter pylori (5). He had made observations of these curved bacilli in samples from the stomachs of sufferers. However, to prove his theory, and fulfil Koch’s postulates, he took the extreme measure of swallowing a dose of the bacteria he had isolated. Sure enough, he developed gastritis, the precursor to ulceration, and proved that the bacteria were indeed the causative agent.

* 1990’s – The dawn of genomics in microbiology

In 1995 Venter and Fleischmann at The Institute for Genomic Research (TIGR) achieved the first complete genome sequence of a microorganism -
Haemophilus influenza (H. influenza) (6). This achievement marked the start of a cascade of projects to sequence the genomes of other microorganisms and heralded a new level of understanding of microbial life. H. influenza can cause ear and respiratory infections, as well as meningitis in children (6). It has a genome of 1,830,137 bp encoding 1,749 genes, fairly typical for a bacterium. Until this time, microbial sequencing had depended on the need for a preliminary genome map onto which sequenced fragments could be mapped. However, for H. influenza, DNA was cut into 1600-2000 bp fragments, cloned into plasmids and a few hundred base pairs sequenced from each fragment end. The resulting 24,304 overlapping fragments were then assembled by the TIGR assembler, with assistance from some longer fragments to help place repetitive or identical sequences. At the time the project cost thousands of pounds and took around a year to complete. With advances in sequencing technology, a complete genome can now be sequenced for under £100 and in a matter of hours, testament to how far we have come in such a short time.

* 2000’s – Bacteria have “immune systems” too

In 2005, Mojica from the Univ. Alicante proposed CRISPR as part of a bacterial “adaptive immune system” after identifying homology of spacer sequences to viral and plasmid DNA (7). He adopted the name from Ruud Jansen who first used the term in print in 2002. Another group from Univ. Paris-Sud also independently published similar findings in the same year (8). The area attracted great interest and, also in 2005, Bolotin published findings regarding a large protein with nuclease activity, cas9, which is now the centre of many gene editing efforts, and the protospacer adjacent motif (PAM), which is required for target recognition (9). In 2006 Koonin used computational analysis to form a hypothetical scheme for CRISPR cascades as bacterial immune systems based on inserts homologous to phage DNA in the natural spacer array. In 2007, this prediction was confirmed by work on Streptococcus thermophilus, commonly used in yogurt production where phage attack is problematic, by Horvath. They integrated new phage DNA into the CRISPR array and showed that it enabled them to fight off the next wave of attacking phage (10). CRISPR has proved to be a burgeoning area of discovery and a multitude of papers elucidating the mechanisms of their action and ways to exploit their properties have ensued over subsequent years.

* 2010’s – Creating something out of nothing

In 2016, a team lead by the biologist Venter of the J. Craig Venter Institute, were the first to create a completely synthetic organism, dubbed syn3.0 (11). It is a bacterium that contains only the genes required to live, eat and self-replicate, and has a smaller genetic code than any naturally occurring bacteria known. Syn3.0 contains 473 genes, 324 of which have known functions but 149 of which still remain a mystery past being essential for life. The project started back in 1995 with the sequencing of Mycoplasma genitalium which, at 525 genes, was thought to have the smallest bacterial genome (12). What if you could make an organism with the minimal code necessary for life? A breakthrough in 2010 whereby Venter reconstructed the genome of another Mycoplasma species synthetically outside the bacteria, meant the team had a vessel in which to test their synthetic genome, adding and removing genes and monitoring the effects. It is hoped that the production of syn3.0 could help answer questions about early life and help other researchers to better understand the genomes of more bacterial species.

References:
1. Zinder, N and J. Lederberg, 1952. Genetic exchange in Salmonella. J. Bacteriol. 64: 679-699.
2. Jacob, F., D. Perrin, C. Sanchez, and J. Monod. 1960. L’operon: Groupe de genes a l’expression coordonne par un operateur. Compt. Rendu. Acad. Sci. 245:1727-1729.
3. Riedel S. 2005. Edward Jenner and the history of smallpox and vaccination. Proc (Bayl Univ Med Cent). 18(1):21-5.
4. Fenner et al. 1988. Smallpox and its Eradication, History of International Public Health. No. 6. WHO.
5. Warren, J. R., and B. Marshall. 1983. Unidentified curved bacilli on gastric epithelium in active chronic gastritis. Lancet 1:1273.
6. Fleischmann et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
7. Mojica et al. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60:174-82.
8. Pourcel et al. 2005. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA and provide additional tools for evolutionary studies. Microbiology 151:653-663.
9. Bolotin et al. 2005. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151:2551–2561.
10. Barrangou et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712.
11. Hutchison et al. 2016. Design and synthesis of a minimal bacterial genome. Science 351(6280):aad6253.
12. Fraser et al. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397-403.