Inspired by the recent post about "quasispecies:"

I have been bothered recently by the following problem: why do species
of genetic uniformity exist at all (or do they?)? This first came up
when I saw a Nature paper describing live bacteria extracted from a
supposedly 250-million-year-old salt crystal whose 16S RNA was 99%
identical to marismortui bacteria (ref below). What? Are the bacteria
the same now as 250 million years ago? But there is a further
question: given the assumptions of evolution, why should there be any
bacterium whose genome is the same as any other, assuming that
equivalent codons are really equivalent (or at least roughly so), and
that even at the protein level, there is such a thing as "neutral
drift?" After all, we even see in our lab cultures that they (at least
e coli) mutate fairly frequently, so why is there such a thing as "e
coli" at all, at least at the nucleotide level? I don't think we
usually say that each bacterial species is totally optimized in all
its features, do we? Even assuming that every single protein must be
just so, shouldn't there be as many species of e coli as there are
possible genomes encoding the same protein set, i.e. some extremely
large number? Why is there any uniformity at all? Or IS there--maybe
the bacteria too are only quasispecies...? And maybe also...

JPK




Nature 407, 897-900 (19 October 2000) | doi:10.1038/35038060; Received
15 November 1999; Accepted 4 July 2000

Isolation of a 250 million-year-old halotolerant bacterium from a
primary salt crystal

Russell H. Vreeland1, William D. Rosenzweig1 & Dennis W. Powers2

Department of Biology, West Chester University, West Chester,
Pennsylvania 19383 , USA
Consulting Geologist, Box 87, Anthony, Texas 79821, USA
Correspondence to: Russell H. Vreeland1 Correspondence and requests
for materials should be addressed to R.H.V. (e-mail: Email:
[log in to unmask]).

Top of page
Bacteria have been found associated with a variety of ancient
samples1, however few studies are generally accepted due to questions
about sample quality and contamination. When Cano and Borucki2
isolated a strain of Bacillus sphaericus from an extinct bee trapped
in 25–30 million-year-old amber, careful sample selection and
stringent sterilization techniques were the keys to acceptance. Here
we report the isolation and growth of a previously unrecognized
spore-forming bacterium (Bacillus species, designated 2-9-3) from a
brine inclusion within a 250 million-year-old salt crystal from the
Permian Salado Formation. Complete gene sequences of the 16S ribosomal
DNA show that the organism is part of the lineage of Bacillus
marismortui and Virgibacillus pantothenticus. Delicate crystal
structures and sedimentary features indicate the salt has not
recrystallized since formation. Samples were rejected if brine
inclusions showed physical signs of possible contamination. Surfaces
of salt crystal samples were sterilized with strong alkali and acid
before extracting brines from inclusions. Sterilization procedures
reduce the probability of contamination to less than 1 in 10 9.

2012/1/24 Darren Hart <[log in to unmask]>:
> I think the explanation is this:
> The source is natural viral RNA which is a mixture of naturally mutated
> sequences (e.g. flu forms such a quasispecies)
> See:
> http://www.virology.ws/2009/05/11/the-quasispecies-concept/
>
> The pooled RNA has an average sequence that you see when you sequence the
> pooled cDNA (individual mutations are hidden by the averaging effect of
> having many sequences present).
>
> But when you clonally separate DNA molecules by transformation (1 plasmid
> enters 1 cell to yield 1 colony), you see each individual molecule
> represented 100% in the sequencing chromatogram from the plasmid DNA that
> you have isolated from colonies.
>
> This is effect is commonly observed when sequencing influenza virus isolates
> from patients. It will have nothing to do with the E. coli strain. You can
> avoid it completely by using gene synthesis.
>
> Darren
>
>
>
> 2012/1/24 Rubén Sánchez Eugenia <[log in to unmask]>
>>
>> Dear everyone,
>>
>> I am trying to clone a viral protein in the E. Coli BSJ strain and i am
>> having some problems.
>>
>> I start from the viral RNA carrying out a reverse transcription and PCR
>> (RT-PCR) to obtain the protein cDNA. When I sequence this cDNA to check for
>> mutations, there are no mutations. So the RT-PCR works fine.
>>
>> Then, I digest the cDNA and I ligate it with a pET plasmid to transform
>> the E. Coli BSJ strain. I get recombinant colonies (checked by colony-PCR)
>> but when I sequence them I get various mutations (aprox. 2 miss-sense) on
>> the inserted cDNA. Furthermore, these mutations are different among
>> different transformations and even among colonies of the same plate (in the
>> same transformation).
>>
>> Maybe these mutations are produced by the cell (because of the lack of
>> mutations in the cDNA) but these E. Coli clonning strains are supposed to be
>> "optimized" to prevent the insertion of mutations. So I have no idea about
>> what may be the problem.
>>
>> I hope you could help me. Thank you.
>>
>> Best regards,
>>
>> --
>> ---------------------------------------------------
>> Rubén Sánchez
>>
>>
>
>
>
> --
> **********************************************************************
> Dr. Darren Hart,
> Team Leader
> High Throughput Protein Lab
> Grenoble Outstation
> European Molecular Biology Laboratory (EMBL)
> **********************************************************************
> www.embl.fr/research/unit/hart/index.html
>
> For funded access to ESPRIT construct screening via EU FP7 PCUBE:
> http://tinyurl.com/ydnrwg4
>
> Email: [log in to unmask]
> Tel: +33 4 76 20 77 68
> Fax: +33 4 76 20 71 99
> Skype: hartdarren
> Postal address: EMBL, 6 rue Jules Horowitz, BP181, 38042 Grenoble, Cedex
> 9, France
> **********************************************************************



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Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [log in to unmask]
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