Molecular Biology:

"Hiding in Plain Sight",

Miriam I. Rosenberg and Claude Desplan

Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA.

E-mail: cd38@nyu.edu

The roles of RNA in protein synthesis are well known—as a template for translation of cellular proteins and as ribosomal and transfer RNA (tRNA). However, more recent studies have elucidated the intricate functions of other abundant types of RNAs, such as micro RNAs (miRNAs) and small inhibitory RNAs (siRNAs), which control the expression of target messenger RNAs (mRNAs) (1). Despite this extensive catalog of functional RNAs, many transcribed RNAs still lack an obvious protein product or the characteristic structure of known functional RNAs. Except for a few examples involved in gene silencing and imprinting (2, 3), the importance of so-called long noncoding RNAs (lncRNA) remains controversial (4, 5). On page 336 of this issue, Kondo et al. (6) show that an RNA called polished-rice (pri) has features of a lncRNA, but encodes tiny peptides that control gene expression during development in the fruit fly Drosophila melanogaster.

Read the Full Text:
   Figure 1: Micropeptides.
References:
Additional References:
Conclusions from Euchromatin, Embryomas, and Entropy:
Further Topics:

The pri gene was first identified as millepattes (mlpt) in the flour beetle, Tribolium, by virtue of its developmental role in body patterning (7). The same gene is responsible for the defects in leg, embryonic epidermis, and respiratory system of pri mutants [(also called tarsal-less (tal) in Drosophila (8, 9)]. Surprisingly, the gene underlying these important functions does not encode a single large protein or functional RNA, but rather four or five small peptides of 11 to 32 amino acids that are highly conserved among insects (10). Unlike many bioactive peptides, Pri peptides are not processed from a longer precursor protein. Instead, the pri RNA is polycistronic and encodes several redundant units that are independently translated.

Figure 1: Micropeptides.

Figure 1: Micropeptides.

Several small peptides are expressed from the lncRNA pri. In Drosophila, proteolytic cleavage of the transcription factor Svb is directed by small Pri peptides. Other RNA, such as lncRNA or mRNAs with short open reading frames, may also generate peptides that direct cleavage or other modifications of target proteins.

CREDIT: C. BICKEL/SCIENCE

How does pri work with svb to differentiate trichomes in the epidermis? The critical interaction requires pri as a temporal switch during trichome formation. Pri peptides direct removal of a large amino-terminal fragment of the Svb protein that contains a transcriptional repression domain. This removal switches Svb from a repressor to an activator of transcription (see the figure). In the absence of pri, Svb retains its repression domain, and thus prevents trichome formation. The ability of Pri peptides to direct proteolytic cleavage of a transcription factor within the same cell is a new function for bioactive peptides. How these peptides impart specificity to a protease (and to which protease) is still not clear.

Because the pri/tal/mlpt gene is highly conserved and is found in all insects, it is not merely a derived character of Drosophila. Furthermore, pri mutant flies have additional phenotypes that do not require svb, so Pri peptides likely act on other proteins as well. Remarkably, despite the sequence conservation of Pri peptides, their function in insects appears to have evolved rapidly: pri/tal does not seem to play a role in embryo segmentation in flies as mlpt does in beetles. This highlights the exciting possibility of a new class of regulatory molecules with diverse and dynamic functions that may be hiding in plain sight.

Because of their small size, Pri peptides cannot be identified by genome annotation or by protein prediction algorithms whose threshold of detection is about 100 amino acids. Like the miRNA genes lin-4, let-7, or bantam, the pri/tal/mlpt gene was identified by classical forward genetics (starting with a mutant phenotype and then identifying the underlying gene). One exciting question that remains unanswered is how many functional peptides might be hidden among RNAs. Some might be encoded by short open reading frames found in 5'-untranslated regions of mRNAs. An estimated 40% of Drosophila mRNAs contain such uORFs and some show signs of evolutionary conservation, suggesting that they are translated (13). Ribosome profiling, which sequences ribosome-bound mRNAs, has validated the translation of a number of uORFs in yeast (14), and vertebrate genomes have similar percentages of uORF-containing transcripts, which await similar analysis (15). When added to the lncRNAs of unknown function, there are many places to look for additional regulatory peptides like Pri. If only some of these transcripts encode active peptides that possess multiple protein substrates, then the scope of posttranslational regulation could quickly expand.

Small functional peptides could evolve rapidly. Random mutations that introduce start codons in existing lncRNAs (or within untranslated regions of coding mRNAs) could generate small peptides that are easily selected to perform a specific function. Many proteins (like Svb) have multiple functional domains, and proteolytic cleavage of one of these domains directed by small peptides may alter protein specificity, stability, localization, or function. A simple recognition code whereby small peptides act as adaptors to direct proteolytic machinery to different protein targets would make a small collection of peptides highly serviceable. Adapting such small peptides to target proteins might open the way to new therapeutic approaches (such as antivirals).

Why does nature need yet another mode of gene regulation? The same question was raised for miRNAs and their modulatory role. The ability of small peptides to quickly alter activities of target proteins without elaborate and time-consuming translation of large proteins suggests a niche for these tiny players as temporal switches. Thus, the discovery of a regulatory mechanism for small peptides highlights how a different reading of the same genomes could reveal additional surprises.

References:

    * 1. P. P. Amaral et al., Science 319, 1787 (2008).[Abstract/Free Full Text]

    * 2. J. E. Wilusz et al., Genes Dev. 23, 1494 (2009).[Abstract/Free Full Text]

    * 3. C. P. Ponting et al., Cell 136, 629 (2009). [CrossRef] [Web of Science] [Medline]

    * 4. M. Guttman et al., Nature 458, 223 (2009). [CrossRef] [Web of Science] [Medline]

    * 5. J. L. Tupy et al., Proc. Natl. Acad. Sci. U.S.A. 102, 5495 (2005).[Abstract/Free Full Text]

    * 6. T. Kondo et al., Science 329, 336 (2010).[Abstract/Free Full Text]

    * 7. J. Savard et al., Cell 126, 559 (2006). [CrossRef] [Web of Science] [Medline]

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1. Each cell retains all of its embryonic genes for a lifetime.

2. Controls for embryonic genes are often absent in adults.

3. Uncontrolled embryonic genes can replicate wildly.

4.  Replicating genes participate in  intra-cellular competition.

5.  The basis for gene competition is selective transcription.

6.  MicroRNAs can reprogram embryomic transcription.

7.  Gene reprogramming can produce normal phenotypes.

8.  Normal phenotypes can by-pass chromosomal lesions.

9.  MicroRNA therapy may need to be permanent.

10. Transplantation of microRNAs could be preferred.

http://www.embryomas.net/

1. Pathways within cell genomes involve a flow of information.

2. Information can flow by direct contact or by third parties.

3. Direct contact within whole genomes is difficult to regulate.

4. DNA-DNA direct contects are influenced by agents.

5. Nuclear agents include hydrophilic ionic and hydrophobic conforming ligands.

6. Third parties within genomes involve RNAs and proteins.

7.  RNAs and proteins are easy to regulate or reverse.

8.  Information can be shared, lost, or transformed.

9. System information can be hidden during system isolation.

10.  Local information can be permanently lost during system entropy.

http://www.embryomas.net/

Links to Current Research in Euchromatin:
Links to Euchromatin Activator RNA Reviews:
Links to Euchromatin Activator RNA Research:
Links to Ultrastructural Probes of DNase I-Sensitive Sites:
Links to RNA as a Therapeutic Agent:
Links to Hodgkin Lymphoma Immuno-Pathology:
Links to Activated T-Lymphocyte Immunotherapy:
Links to Medical Systems Biology:
Links to Selective Gene Transcription:
Links to RNA-Induced Epigenetics:
Links to RNA-Induced Embryogenesis:
Links to RNA and Biological Causality:
Links to Reprogramming and Neoplasia:

A Brief History of Activator RNA:

"Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".
(PowerPoint Presentation).

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