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: rvreel...@wcupa.edu). 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 <h...@embl.fr>: > 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 <ruben...@hotmail.com> >> >> 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: h...@embl.fr > 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 > ********************************************************************** -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
