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New Millennium Blog 2-9-22

By Priya DasSarma

So I know it has been a few decades since the millennium started, but I feel like this is as good a time as any to look back and record my thoughts on research and exploration that I have done over time. So here goes – Starting with the year 2000…

This was the much anticipated cusp of the millennium, which for those who are sticklers, does in fact start the following year. I was still raising kids, but was fortunate enough to be involved with the periphery of the sequencing of the first Haloarchaeon ever! Back in those days, we clipped articles by hand from the news papers, that in those days were only available as paper copies. I have “pasted” some clippings below.

So, to put it into context, there was a big race for completely sequencing the first non-viral genome back in the day. It was the pathogen, in 1995: Haemophilus influenza (a Bacterium), followed by the yeast genome (Saccharomyces cerevisiae, a Eukaryote). The first Archaeon sequenced, was Methanococcus jannaschii, a methanogen. At about the same time, the DasSarma laboratory led the effort in collaboration with the Hood laboratory, to sequence Halobacterium halobium or Halobacterium sp. NRC-1 as it is known now.

A quick note on the name issue – you are correct to wonder! Halobacterium is an Archaeon, so should really be Haloarchaeon, and the halobium bit got taken out since there were so many researchers trying to change and rearrange the species (which is NRC-1) with various names – we left behind that battle and just called it sp. – for more on this, see our paper “On the origin of prokaryotic “species”: the taxonomy of halophilic Archaea”. Regarding NRC-1 – this is the abbreviation Ford Doolittle put on the vial of the microbe he gave to Shiladitya DasSarma. It is probably short for NRCCCC-1 (National Research Council Canada Culture Collection). The strain was given to them by Walther Stoeckenius, who collected the sample from San Francisco Bay Salterns, California, USA.

An interesting side note is that Prof Shiladitya DasSarma and his team had already sequenced one of the two plasmids (now known as minichromosomes) and were ready to complete the whole genome considerably earlier. They had approached the TIGR team, that did the Haemophilus influenza genome to do this as a collaboration. The TIGR team politely declined, as they thought that the process would be too difficult due to the high G-C content of the Haloarchaeon. It is true that we know that adenine always pairs with thymine by two hydrogen bonds, while guanine always pairs with cytosine by three hydrogen bonds, making this a harder bond to break. Well, the National Science Foundation did fund the project and by 2000, the genome sequence was complete.

In an effort to bring the community together and to better be able to analyze the sequences, Prof DasSarma assembled a consortium of 43 researchers from 12 laboratories from several countries to focus. This was a big effort, since only about a dozen genomes had been completed at the time and as it turned out, at the time, 36% of the predicted proteins were unrelated to anything sequenced before! He then organized an NSF-sponsored meeting to bring these collaborators together for a face-to-face meeting in Amherst, Massachusetts to discuss. This was the first, wholly NSF-funded genome project.

At the meeting (left) and Leroy Hood, Victor Ng and Shiladitya DasSarma (Right)

It was the very first of its kind and was published on October 24 2000, on the cover of The Proceedings of the National Academy of Sciences, U.S.A. with an added centerfold-out of the genome. Several fundamental discoveries were made and confirmed:

1. Indeed, the 2,571,010-bp genome has a high G-C content: though the two minichromosomes, pNRC100 (191,346 bp, 57.9%) and pNRC200 (365,425 bp, 59.2%) were substantially less GC rich than the chromosome (2,014,239-bp 67.9%).
2. The genome contained 91 IS elements representing 12 families, including 29 on pNRC100 (12), 40 on pNRC200, and 22 on the large chromosome. Two new elements, ISH5 and ISH10, were identified.
3. The NRC-1 proteome is highly acidic (average pI of 5.1), consistent with protein stabilization and adaptation to a high-salt environment

The high GC- content and acidic proteome discovered in this genome sequencing effort has held true ever since for all Haloarchaeal genomes sequenced since.

The story made the news world-wide, from the Amherst Bulletin front page, to the Daily Hampshire Gazette to the BBC. In a very premonition way, Prof DasSarma stated that they could be one day used to develop vaccines and produce useful proteins such as antibiotics as well as for space research, “could contribute to an understanding of how life arose on Earth” or “help scientists recognize evidence of life on other planets in our solar system”, stating that  “What is neat about that is that it expands our notions of what life is.” (Reproduced from article by Michelle Aguilar, with Permission from the Daily Hampshire Gazette, October 10, 2000 below and it was a very monumental feat, and years later, they published the following: A Look Back, By James Bridgman, Friday, October 8, 2010: 10 YEARS AGO: “Scientists at the University of Massachusetts have cracked the genetic code of a prehistoric microorganism so hardy it can survive conditions 10 times saltier than sea water and possibly even the stress of inter-planetary travel. The Halobacterium genetic-mapping project is led by UMass microbiology Professor Shiladitya DasSarma.”) – a historic feat!