Wounded King writes:
think I have made a reasonable case that the choice of sequences incorporated is not non-random in any meaningful sense, beyond perhaps a variable specificity for certain common motifs occurring hundreds of times even in the small genomes of bacteriophages.
I think this paper disagrees with your opinion;
"RNA-guided complex from a bacterial immune
system enhances target recognition through
seed sequence interactions"
Blake Wiedenhefta,b, Esther van Duijnc,1, Jelle Bultemad,1, Sakharam Waghmaree,1, Kaihong Zhoua,1, Arjan Barendregtc,
Wiebke Westphalb, Albert Heckc, Egbert Boekemad, Mark Dickmane, and Jennifer A. Doudnaa,b,f,g,2
aHoward Hughes Medical Institute; bDepartment of Molecular and Cell Biology, University of California, Berkeley, CA 94720; fPhysical Biosciences Division,
Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Department of Chemistry, University of California, Berkeley, CA 94720; gDepartment of
Chemistry, University of California, Berkeley, CA 94720; cBiomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular
Research, Utrecht Institute for Pharmaceutical Sciences, and The Netherlands Proteomics Center, Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands; dElectron Microscopy Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4,
9747 AG, Groningen, The Netherlands; and eDepartment of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield,
Mappin Street, Sheffield S1 3JD, United Kingdom
Contributed by Jennifer A. Doudna, February 24, 2011 (sent for review January 5, 2011)
In the abstract they write;
Prokaryotes have evolved multiple versions of an RNA-guided
adaptive immune system that targets foreign nucleic acids. In each
case, transcripts derived from clustered regularly interspaced short
palindromic repeats (CRISPRs) are thought to selectively target invading
phage and plasmids in a sequence-specific process involving
a variable cassette of CRISPR-associated (cas) genes.
and;
Here we show
that the Csy proteins (Csy1C4) assemble into a 350 kDa ribonucleoprotein
complex that facilitates target recognition by enhancing
sequence-specific hybridization between the CRISPR RNA and complementary
target sequences. Target recognition is enthalpically
driven and localized to a seed sequence at the 5 end of the
CRISPR RNA spacer.
and;
These repetitive elements rapidly expand
in response to phage challenge by site-specifically integrating
short fragments of the foreign DNA at one end of the evolving
CRISPR (3C5). CRISPR adaptation results in sequence-specific
resistance to genetic parasites containing a complementary sequence.
and;
Here we report the discovery of a CRISPR-associated complex
from the PA14 strain of P. aeruginosa. The complex is composed
of a unique set of proteins, which have previously been shown
to be exclusive to and conserved in the Csy subfamily (CRISPR
system yersinia) of CRISPR-mediated immune systems (7, 9).
We show that this complex participates in target recognition by
facilitating sequence-specific hybridization between the crRNA
and complementary targets. Similar to mRNA recognition by
Argonaute proteins during RNA interference (RNAi) in eukar-
yotes, CRISPR target selection is governed by a seed sequence
at the 5 end of the crRNA spacer. Although comprised of distinct
proteins, the stoichiometry and the morphology of the Csy complex
resemble the architecture of the Cascade complex from
E. coli. These findings suggest that large CRISPR-associated
ribonucleoproteins mediate surveillance and target recognition in
diverse CRISPR-mediated immune systems.
Also Shapiro in his book "Evolution a view from the 21st century"
wrote aboult the famous Luria-Delbruck fluctation test that purported to prove that infection could not induce resistance. In fact Shapiro states that what Luria and Delbruck:
" demonstrated was that mutations conferring resistance to a virus that is invariably lethal immediately upon infection do occur prior to selection. They never could disprove the operation of a CRISPR or other infection-triggered resistance mechanism for other viruses, such as temperate bacteriophages. The incorporation of fragments from invading DNA elements for the purpose of self-defense (the CRISPR system has been described as a genomic immune system is a precise example of the kind of dedicated, nonrandom, beneficial change specifically excluded by generations of evolutionary theorists."
In the Kafginov paper http:
http://www.ncbi.nih.gov/pmc/articles/PMC2819186/
The authors wrote;
Thus, during the acquisition of a defensive repertoire, the CRISPR machinery appears to select sequences from the phage genome and incorporate these as novel spacers (Fig. 2B). The selection is not random. Instead, sequence motifs can be detected in proximity to those regions that ultimately become part of the CRISPR, termed proto-spacers. Analysis of spacers newly added to the CRISPR1 locus of independently selected S. thermophilus phage-insensitive mutants identified a short motif (NNAGAAW) directly downstream of the proto-spacer in the phage genome (Deveau et al., 2008). A similar motif was independently observed by Bolotin and colleagues (Bolotin et al., 2005). Interestingly, spacers from CRISPR3, a locus with some divergence from CRISPR1, showed a different downstream motif, NGGNG, near proto-spacers (Horvath et al., 2008). In S. mutans, one CRISPR locus displayed a preference for a short motif 3′ of the proto-spacer, while another CRISPR locus favored a 5′-adjacent motif (van der Ploeg, 2009). Similarly, three different CRISPR families in the archaeal Sulfolobales have distinct 5′ proto-spacer adjacent motifs (PAMs) (Lillestol et al., 2009). Like the repeat and leader sequences, distinct PAMs correspond to specific CRISPR/cas subtypes (see the section on CRISPR/cas co-evolution below). This suggests that spacer acquisition is driven by recognition of phage sequences by subtype-specific proteins in different species (Mojica et al., 2009). However, it also implies that when an individual species harbors multiple CRISPR loci from different subtypes, these represent distinct and compartmentalized resistance systems. In addition to its suggested role in spacer selection, the PAM also appears to be important at the effector stage of defense, since phage can evade resistance to a particular spacer by mutating this nearby motif (Deveau et al., 2008).
And at p.13
However, armed with knowledge of the molecular basis of this response, CRISPR-cas does seem to fit more firmly with a Lamarckian paradigm, in essence because increases in fitness do not rely on random mutations but on a much more specific acquisition of genetic information from environmental sources.
Based on what I have read I believe it shows that the CRISPR System is nonrandom for fitness.
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