Frontiers in Cell Biology: Quality Control
First
paragraph:
“Cells are the basic building blocks of living organisms, and the cell can be
pictured as a very complicated factory of life. In order to maintain an
effective internal regime and to prevent inappropriate attack by external
factors, the cell needs quality
control mechanisms to
identify, correct, and prevent mistakes in its ongoing processes. The
consequences of faulty quality
control range from the cell
death of neurodegeneration to the uncontrolled
cell growth that is cancer”.
Stella
M. Hurtley, Science 1999 December 3; 286: 1881 (in Introduction to
special issue)
Quality Control by DNA Repair
Science 1999 December 3; 286: 1897-1905.
Abstract: “Faithful maintenance of the genome is crucial to the individual and to species. DNA damage arises from both endogenous sources such as water and oxygen and exogenous sources such as sunlight and tobacco smoke. In human cells, base alterations are generally removed by excision repair pathways that counteract the mutagenic effects of DNA lesions. This serves to maintain the integrity of the genetic information, although not all of the pathways are absolutely error-free. In some cases, DNA damage is not repaired but is instead bypassed by specialized DNA polymerases”.
Fragments of the Article: “…No correction procedure is going to be absolutely exact and error-free, but repair of common DNA lesions clearly demands highly accurate performance…”, “…The most frequent DNA lesions are efficiently removed…”, “these restricted procedures require special strategies to function at high accuracy, such as protection of reactive DNA intermediates by protein-DNA interactions, and access to a high-fidelity DNA-copying machine with editing capacity”, “The well-characterized DNA mismatch correction system (J. Jiricny, Replication errors: cha(lle)nging the genome, EMBO J. 17, 6427, 1998) further minimizes replication errors by a systematic survey of newly synthesized strands. In addition, accessory factors such as the DNA helicases encoded by the genes defective in Werner syndrome and Bloom syndrome apparently serve to improve accuracy during DNA elongation, possibly due to resolution of stalled replication forks. Despite all these precautions, occasional misincorporated nucleotides, deletions, and insertions may remain to be expressed as rare mutations.
A comprehensive overview of quality control in DNA would include a discussion of DNA polymerase fidelity and postreplicative mismatch correction and would also consider the damage-responsive cell-cycle checkpoints and the signal transduction systems that lead to cellular effects. Here we focus more closely on the main DNA lesions in human cells and on rapidly accumulating information about the distinct strategies used to repair or tolerate these adducts.
DNA
Lesions
…The key lesions can generally be removed by both a main repair pathway and one or more backup pathways… This mode of DNA quality control seems well suited for removing a rare but highly mutagenic DNA lesion by the energetically expensive approach of sacrificing an entire protein molecule for each lesion corrected.”.
Base
Excision Repair
Our recent data on uracil-DNA glycosylase activities in cell extracts from UNG knockout mice have revealed a fifth distinct activity of this type, emphasizing that correction of uracil in DNA is a major biological problem that demands substantial and partly overlapping activities to retain a high extent of DNA quality control. Even in nongrowing cells, expedient removal of uracil from DNA appears necessary to avoid transcriptional base substitution that would generate mutant proteins and phenotypic changes (A. Viswanathan, H. J. You, P. W. Doetsch, Phenotypic Change Caused by Transcriptional Bypass of Uracil in Nondividing Cells, Science 284, 159, 1999). Additional distinct uracil- or thymine-DNA glycosylases, not clearly related to mammalian enzymes, have been described in thermophilic Archaea; such organisms also have DNA polymerases with read-ahead functions that stall incorporation when a uracil residue is detected in the template strand (M. A. Greagg, et al., A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil, Proc. Natl. Acad. Sci. U.S.A. 96, 9045 (1999)).
…The versatility of this DNA glycosylase means that absolute discrimination between normal and damaged bases is particularly difficult…
…Temporary inefficiency in this process during early mammalian development could explain the origin of several human syndromes such as Huntington's disease, which are associated with expansion of triplet repeats in relevant genes…
… Nevertheless, the consecutive ordered interactions may serve to protect reaction intermediates and ensure efficient completion of the correction process after the initial recognition of DNA damage.
Repair
of Strand Breaks
… A surprisingly large number of nuclear proteins bind specifically to double-strand breaks. Besides protecting the lesion, they apparently serve to signal the presence of such damage and to instruct cell-cycle control proteins about the imminent hazard…
…Repair of double-strand breaks by homologous recombination with another allele can be achieved with high fidelity…
…The mechanism of DNA damage recognition in NER (Nucleotide Excision Repair) is a long-standing problem. The efficiency of repair of different kinds of lesions varies over several orders of magnitude. To a first approximation this roughly correlates with the extent of distortion caused by an adduct. However, to be well-repaired by NER, a lesion must both distort the structure and covalently modify the DNA. Distortion alone is not sufficient, given that very disruptive lesions such as small loops and mismatches are repaired very poorly, if at all (M. T. Hess, U. Schwitter, M. Petretta, B. Giese, H. Naegeli, Bipartite substrate discrimination by human nucleotide excision repair, Proc. Natl. Acad. Sci. U.S.A. 94, 6664 (1997); J. G. Moggs, D. E. Szymkowski, M. Yamada, P. Karran, R. D. Wood, Nucleic Acids Res. 25, 480 (1997); D. Mu, et al., Mol. Cell. Biol. 17, 760, 1997). Conversely, nondistorting adducts such as seemingly harmless modifications of sugar residues are readily removed, if the altered nucleoside is placed within a mismatch (M. T. Hess, H. Naegeli, M. Capobianco, J. Biol. Chem. 273, 27867, 1998). The best way to explain these observations currently is by a "bipartite" or two-step model for recognition. In the first step, a distortion is recognized; in the second, the damaged strand and chemical alteration are located.
…UV-DDB expression clearly contributes to the efficiency of pyrimidine dimer
removal in cells, but its role in DNA repair is enigmatic (B. J.
Hwang, J. M. Ford, P. C. Hanawalt, G. Chu, Expression of the p48 xeroderma
pigmentosum gene is p53-dependent and is involved in global genomic repair, Proc.
Natl. Acad. Sci. U.S.A. 96, 424, 1999); D. P. Batty and
R. D. Wood, Gene, in press). One possibility is that UV-DDB is
specialized for detecting damage within chromatin (V. Otrin, M.
McLenigan, M. Takao, A. Levine, M. Proti
,
J. Cell Sci. 110, 1159, 1997)….
… One fascinating feature of mammalian NER proteins is that most of them
have dual functions, participating in other aspects of DNA
metabolism. For example, RPA is the major single-strand DNA binding
protein in cells, necessary for semiconservative replication and
recombination as well as NER….
… DNA replication and transcription take place in localized factories within cell nuclei (P. R. Cook, The Organization of Replication and Transcription, Science 284, 1790, 1999), which seems reasonable for processes that require a systematic progression along DNA. Repair might operate more efficiently, however, by relying on diffusion of factors through the nucleus and formation of transient complexes at sites of damage only when correction is needed. In cell-free lysates, NER is a distributive process, and this is also likely to be true within nuclei (D. E. Szymkowski, M. A. N. Hajibagheri, R. D. Wood, J. Mol. Biol. 231, 251 (1993); S. J. Araújo and R. D. Wood, Mutat. Res. 435, 23, 1999)…
Accuracy
in DNA Gap Filling
Replicative DNA polymerases bind efficiently to DNA and copy the template in a processive reaction of high fidelity, approaching only one error in 105 nucleotides… During NER, gaps of ~30 nucleotides are filled in by one of these enzymes (R. Wood and M. Shivji, Carcinogenesis 18, 605 (1997); M. E. Budd and J. L. Campbell, Mutat. Res. 384, 157, 1997), so the reaction should proceed at a level of faithfulness similar to that seen in replication.
… By this strategy, high-fidelity DNA synthesis of the lagging
strand can be achieved without the need for a 3' exonuclease
activity to complement the role of POL 
…
… Then, following the same strategy as used by the E. coli
Pol III holoenzyme where the dnaE and dnaQ genes
encode separate subunits for polymerization and editing (R. H.
Scheuermann and H. Echols, Proc. Natl. Acad. Sci. U.S.A. 81,
7747, 1984), a distinct mammalian 3' exonuclease can remove the
mismatched residue, creating a second opportunity for correct gap-filling.
A human homolog of the DnaQ 3' exonuclease was identified recently
that allows error-free processing of mistakes during DNA short-patch
gap filling by POL 
in
vitro, making the new enzyme the main candidate for an editing role
during BER (M. Höss, et al., EMBO J. 18, 3868 (1999); D.
J. Mazur and F. W. Perrino, J. Biol. Chem. 274, 19655, 1999).
The high amount of hydrolytic DNA depurination in human cells combined
with the low accuracy of POL makes
such a proofreading step during BER (Base Excision Repair)
obligatory to avoid an unacceptably high spontaneous mutation rate
caused by synthesis errors during correction of endogenous DNA
damage.
DNA
Polymerases That Bypass Damage
Cell-cycle checkpoints are often thought of as a mechanism for cells to repair damage in their DNA before replication or cell division proceeds. But this is an oversimplification, and it is becoming widely appreciated that cells can tolerate much damage in their genomes without removing it… Normal cells divide with an even larger amount of UV damage (G. Spivak and P. C. Hanawalt, Biochemistry 31, 6794, 1992). Pyrimidine dimers are effective blocks to the progression of replicative DNA polymerases, so how is such tolerance achieved? It is now clear that part of the solution is supplied by specialized enzymes that can bypass DNA damage and extend replication forks through damaged sites.
… it is not clear why cells retain both mutagenic and
nonmutagenic bypass polymerases for the same type of damage. Perhaps
some bypass polymerases are reserved for lesions that are
particularly difficult to traverse or for cases where coding
information has been completely lost.
Cancer
and Quality Control by DNA Repair
The
existence of human diseases associated with defects in DNA repair graphically
illustrates the importance of this process of quality control. The disorder
XP shows the key role of NER in human avoidance of skin cancer.
Inherited diseases associated with altered processing of
double-strand breaks such as ataxia telangiectasia and Nijmegen
breakage syndrome underline the relevance of defense pathways against
other types of carcinogenic DNA damage. Although complete disruption
of BER seems to be incompatible with viability, it remains possible
that mutations leading to partially reduced function of this repair
pathway might be found in humans. A systematic study of human
polymorphisms in DNA repair genes (H. W. Mohrenweiser and I. M.
Jones, Mutat. Res. 400, 15 (1998); M. Cargill, et al., Nature
Genet. 22, 231,1999) should reveal the extent to which mutations in repair
genes are a risk factor for cancer in the general population.
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And
so as astounding is each one of the next steps in the process for the
production of proteins, next we can see the abstracts of the next review
articles in the molecular Quality Control process:
Setting the
Standards:
Quality Control in the Secretory Pathway.
Science 1999 December 3; 286: 1882-1888.
A variety of quality control mechanisms operate in the
endoplasmic reticulum and in downstream compartments of the secretory pathway
to ensure the fidelity and regulation of protein expression during
cell life and differentiation. As a rule, only proteins that pass a
stringent selection process are transported to their target
organelles and compartments. If proper maturation fails, the
aberrant products are degraded. Quality
control improves folding
efficiency by retaining proteins in the special folding environment of
the endoplasmic reticulum, and it prevents harmful effects that
could be caused by the deployment of incompletely folded or
assembled proteins.
And also:
Quality Control Mechanisms During Translation
Posttranslational
Quality Control
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