Re: Why are RNases more prevalent than DNases?

Sharon,

The answer to your question is related to the difference in the lifetime of 
individual DNA and RNA molecules in a cell, and how their longevity is 
maintained or regulated.  DNA is first and foremost a medium for storing 
genetic information; individual molecules of DNA survive for the duration 
of a cell's lifecycle.  Damage is repaired by the appropriate repair 
mechanisms, but by and large an individual DNA molecule must remain 
unchanged.  On the other hand, the longevity of RNA in vivo is quite short, 
relative to DNA.  While ribosomal RNA (rRNA) may be long-lived, as an 
integral component of the ribosomes, other RNAs often are actively degraded 
within minutes of being transcribed.  This is especially true in regards to 
messenger RNA (mRNA).

The discussion is complicated by the fact that control mechanisms differ 
between prokaryotic systems (bacterial) and eukaryotic systems (higher 
organisms).  In bacteria, mRNA is transcribed and translated in a single 
cellular compartment, allowing for the two process to occur simultaneously. 
 Before transcription is completed, ribosomes bind to the growing mRNA and 
begin translation.  After a short period of time, RNA endonucleases begin 
to nick the mRNA at the 5' end, preventing additional ribosomes from 
binding, even before transcription or translation is completed.  Generally, 
only a few protein molecules are made from a single mRNA before it is 
degraded, with the whole process lasting only a few minutes.  In a 
eukaryotic cell transcription and translation are physically separated 
process, with mRNA synthesis and processing occur in the nucleus, and with 
translation occurring in the cytoplasm.  The lifetime of mRNA in eukaryotes 
is typically on the order of hours to a day rather than minutes, but is 
still quite short compared to DNA.

The comparatively short lifetime of mRNA, relative to DNA, is believed to 
have evolved as a means of regulating rates of protein synthesis.  Remember 
that rates of protein synthesis are a function of both translational 
activation and inactivation.  Translational activation is a fairly 
complicated subject and varies depending on the system.  In general, 
transcription of mRNA is initiated through binding of transcription factors 
to promoter sequences on DNA, followed by recruitment of the appropriate 
RNA polymerase.  The pre-mRNA product of transcription is processed 
(introns are excised, the 5'-end is capped, the 3'-end is polyadenylated), 
the mature mRNA is transported to the cytoplasm, then translated by the 
ribosomes.  On the other hand, down-regulation of translation is 
universally a function of the lifetime of mRNA.  In both prokaryotes and 
eukaryotes, translation of a particular gene is arrested through 
degradation of mRNA by RNases.  Once in the cytoplasm, protein will 
continue to be translated from a single mRNA until the mRNA is actively 
degraded.  The overall rate of protein biosynthesis is therefore a balance 
between RNA synthesis and degredation.  It is commonly accepted that RNA 
degredation occurs at a relatively fixed rate, with transcriptional control 
being mediated by ragulation of RNA synthesis.  RNases are ubiquitous in 
the cell, at relatively constant concentrations, giving rise to a uniform 
rate of mRNA degredation within a cell independent of the protein sequence 
a particular RNA encodes.

The process and rates of RNA degradation of prokaryotic and eukaryotic 
systems differ in detail, but are superficially similar.  RNases are of two 
basic types; endonucleases can cleave in the middle of an RNA molecule, 
while exonucleases degrade RNA from the end of a molecule.  Initially, RNAs 
are protected from being degraded by exonucleases due to the presence of 
end-capping motifs.  Therefore, regulated degradation of an RNA molecule 
begins by a cleavage event from an RNA endonuclease producing an unmodified 
free end, which is quickly targeted by RNA exonucleases.  The precise 
end-capping motifs and the time-frame for RNase activity again vary between 
prokaryotes and eukaryotes, but the basic architecture is the same.  Note 
that RNases exist that have other specific functions, such as RNase H, 
which acts to cleave the RNA component of RNA-DNA hybrids during DNA 
replication.

Common DNases are generally those that are unique to prokaryotes, though 
eukaryotic DNases are known to exist (in the nucleoside, for example).  
DNases are generally also classified as having either exonuclease or 
endonuclease activity.  In prokaryotes, their function is typically one of 
defense, aiding in the degradation of foreign DNA.  Briefly, bacteria 
methylate their DNA as a means of differentiating their own DNA from 
foreign DNA.  Methylation protects a DNA from being cleaved by DNases with 
endonuclease activity, termed restriction endonucleases or restriction 
enzymes. The process of methylation occurs slowly, relative to the rate of 
DNA replication.  The methyl group serves as a tag so the cell can 
recognize which strand of DNA was the parent strand (the methylated one) 
from the daughter strand (non-methylated).  In the case of a replication 
error, the DNA damage control proteins know to change the base on the new 
strand of DNA as it has not yet been methylated.  Similarly, when foreign 
DNA invades a cell, it generally is not methylated.  In the end, the 
restriction endonucleases serve to nick either foreign DNA or a segment of 
DNA containing replication errors, followed by degradation of the nicked 
DNA by DNA exonucleases.

In eukaryotes, the DNA damage repair machinery is a bit more sophisticated, 
and a bit outside the scope of this discussion, so I won't go into it here. 
 While doing some background reading to help answer your question, I did 
learn that two of the more common eukaryotic DNases, DNAse I and DNAse II, 
are thought to be involved in apoptosis.  Presumably, their function is one 
of fragmenting chromosomal DNA beyond repair while other factors involved 
in apoptosis (such as ubiquitin and its function in directed protein 
degradation) are shutting down other major cellular functions, all of which 
lead to cell death.

In summary, RNases are ubiquitous and are continuously degrading RNA in a 
cell.  DNases are not as prevalent and are needed only intermitently in the 
life cycle of a cell.  The empirical observation is, when working with RNA, 
occasional RNase contamination is observed any time protein contamination 
may have ocurred.  From personal experience, it is true that RNases have 
appeared in my own samples, apparently through dust, cat hair, fingers, or 
the wind.  I don't know of any occasion when similar DNase contamination 
may have occurred.


    Suggested reading:

        "Genes VII", Benjamin Lewin, New York: Oxford University Press,
                Call Number: QH430.L487 1999

        "Molecular cloning : a laboratory manual",  Maniatis, Fritsch,
                and Sambrook. Cold Spring Harbor Laboratory Press,
                Call Number: QH442.2 .M26 1982

        "The RNA world" edited by R. F. Gesteland, T. R. Cech, 
                J. F. Atkins. Cold Spring Harbor Laboratory Press,
                N.Y., c1999.  Call Number: QP623 .R6 1999


Good luck with your experiments,
Dr. Jim Kranz