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ScienceWeek
MOLECULAR BIOLOGY: ON POSTRANSLATIONAL PROTEIN MODIFICATION
The following points are made by Benjamin G. Davis (Science 2004 303:480):
1) One of the surprises of the complete first draft of the human genome was that only about 30,000 genes were found -- only about two times as many as in the fly or worm. However, human complexity is not simply a result of the direct protein products of genes. A higher order of complexity can be added after a gene has been translated into the corresponding protein. Recent advances in mimicking these modifications are helping to elucidate the role of the modifications and hold great promise for future pharmaceuticals.
2) Genomes of more complex species typically contain more enzymes and proteins involved in posttranslational modifications of proteins than do the genomes of simpler organisms. The most widespread and complex form of posttranslational modification, glycosylation, requires about 1% of genes (1), yet is typically absent in simple prokaryotic organisms such as bacteria.
3) Posttranslational modifications range from the widespread (such as glycosylation, phosphorylation, ubiquitination, and methylation) to the obscure (such as glutathionylation, hydroxylation, sulfation, transglutamination, and epimerization). Their effects often fundamentally alter protein function. For example, posttranslational modification of proline residues in the transcription factor HIF-alpha (the alpha subunit of the hypoxia-inducible factor) is a key oxygen-sensing mechanism within cells (2), and phosphorylation cascades are a central part of intracellular signaling (3).
4) Why are proteins altered after translation, away from the typically tight control of the gene expression process? One reason may be that it is far easier to create a spectrum of slightly different proteins by taking one basic protein scaffold and fine-tuning or even entirely switching its properties, than to build each protein from scratch just to find that it may not be needed at a given time. Posttranslational modifications create a dynamic combinatorial library of properties that can rapidly respond to systemic stimuli such as oxygen levels or hormonal concentrations. This flexibility may, however, also be turned against us. A recent study found that HIV uses a dynamically changing "shield" of posttranslational glycosylation to evade our immune systems (4).
5) The dynamic complexity of posttranslational modification is often difficult to elucidate in the laboratory. Working out the role of each (sometimes very minor but important) protein component requires abundant sources and extensive purification. Furthermore, to continue to precisely exploit the power of proteins in therapeutics requires the creation of pure protein drugs (most today are sold as mixtures). Methods for creating artificial posttranslational modification mimics may provide a solution to both of these problems (5).
References (abridged):
1. J. B. Lowe, J. D. Marth, Annu. Rev. Biochem. 72, 643 (2003)
2. P. Jaakkola et al., Science 292, 468 (2001)
3. J. A. Pitcher, N. J. Freedman, R. J. Lefkowitz, Annu. Rev. Biochem. 67, 653 (1998)
4. P. D. Kwong et al., Nature 420, 678 (2002)
5. A. Haselbeck, Curr. Med. Res. Opin. 19, 430 (2003)
Science http://www.sciencemag.org
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ON EPIGENETICS
The following points are made by Judith Bender (Current Biology 2002 12:R412):
1) Epigenetic changes in gene expression have fascinated researchers over several decades. These processes have received particular attention in plants, where they can result in beautiful variations in conspicuous phenotypes such as pigmentation. Epigenetic control is also a key issue in the development of transgenic plants with appropriate expression from newly introduced transgene segments.
2) The term "epigenetic" refers to heritable gene expression patterns determined by how the DNA of a gene is packaged rather than its primary DNA sequence. Within tightly packed DNA, genes are not readily available to the transcription machinery and are poorly expressed. Normally the patterns of DNA packaging are carefully controlled to give predictable patterns of gene expression. However, the process can occasionally go awry to cause altered gene expression.
3) In higher organisms, DNA is packaged into the nucleus of the cell by association with histone proteins; this DNA-protein complex is "chromatin". Some regions of the genome are loosely packaged into "euchromatin", whereas other regions are tightly packaged into "heterochromatin". One factor that determines chromatin patterning is modification of histone proteins by attachment of small chemical groups to particular amino acid side chains. Specific patterns of histone modification are thought to recruit specific chromatin remodeling proteins that direct either heterochromatin or euchromatin formation.
4) In mammalian and plant genomes, chromatin patterning is also determined by the attachment of methyl groups to cytosine residues in the DNA by cytosine methyltransferases. When a region of genomic DNA has cytosine methylation it is typically assembled into heterochromatin. Methylated DNA appears to recruit methyl-DNA binding proteins, which in turn recruit histone-modifying enzymes and chromatin-remodeling factors necessary for heterochromatin formation. Cytosine methylation is a fundamental epigenetic mark that can be maintained after each round of DNA replication because the template strand of DNA will retain the modification. Although changes in the cytosine methylation mark often correlate with epigenetic variation, there are also likely to be cases where chromatin changes occur independently of methylation.
5) In mammals, DNA methylation marks are reprogrammed during early embryogenesis and altered methylation patterns are not usually transmitted to progeny. In plants, however, it seems that DNA methylation changes can persist throughout development and can be inherited between generations.
Current Biology http://www.current-biology.com
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ON RNA SILENCING
The following points are made by M. Matzke et al (Science 2001 293:1080):
1) RNA silencing is a new field of research that has coalesced during the last decade from independent studies on various organisms. Researchers who study plants and fungi have known since the late 1980s that interactions between homologous DNA and/or RNA sequences can silence genes and induce DNA methylation. The discovery of RNA interference (RNAi) in Caenorhabditis elegans in 1998 focused attention on double-stranded RNA as an elicitor of gene silencing, and indeed many gene silencing effects in plants are now known to be mediated by double-stranded RNA.
2) RNA interference is usually described as a post-transcriptional gene-silencing phenomenon in which double-stranded RNA triggers degradation of homologous messenger RNA (mRNA) in the cytoplasm. However, the potential for nuclear double-stranded RNA to enter a pathway leading to epigenetic modifications of homologous DNA sequences and silencing at the transcriptional level -- that potential does exist.
3) Although the nuclear aspects of RNA silencing have been studied primarily in plants, there are hints that similar RNA-directed DNA or chromatin modifications might occur in other organisms as well. In general, RNA silencing is proving to be useful for the study of functional genomics in invertebrates and plants, but routine RNA interference might also be possible in mammalian cells, where double-stranded RNA normally elicits a global shutdown of protein synthesis, by direct injection of small interfering RNAs.
Science http://www.sciencemag.org
ScienceWeek http://scienceweek.com
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