Might this apply?

A recent article in RNA – “The exozyme model: A continuum of functionally distinct complexes” – provides at once a timely review of exosome structure and function, and an interesting hypothesis that attempts to explain some interesting features of the exosome as it is found in different eukaryotes.

Recall that the exosome is the term for a (THE) RNA degrading machine in eukaryotes, and that it is analogous in many ways to the degradosome in bacteria.  Over the years, various and sundry exosome subunits have been implicated by genetics or biochemistry in numerous RNA processing and degrading events or systems.  However, there are differences, in terms of subunit composition and activity, between different organisms.  Because of these differences (that I won’t list here – Kiss and Andrulis do an excellent job that would take thousands of words to summarize), the authors of the cited review propose that the “exosome” is better thought of as a collection of “exozymes”, all of which share some subset of the subunits that collectively are usually associated with the conceptual exosome. In the authors’ own words:

Cleveland Rocks!

Not just the Rock and Roll Hall of Fame.  Last weekend, a group of midwestern RNA scientists gathered for the annual Rustbelt RNA Meeting in Cleveland. (There’s a clever pun hidden in the name, one that may fall by the wayside in the next year or so.)

Here is a link to the abstracts.  So readers can take a peek into just what excites RNA scientists.  Enjoy.

PS – just out of curiosity, does the name “Rustbelt” carry negative connotations for readers here?  Just wondering.

Jack of all trades

One of the more intriguing enzymes that handles RNA is polynucleotide phosphorylase (PNPase).  This enzyme is a phosphorolytic 3’->5’ exonuclease; that means that it acts on the 3’ end of an RNA chain and moves towards the 5’ end, and that it adds phosphate (as opposed to water) to the broken phosphodiester bond.  This means that the products of the nucleolytic reaction are a shortened RNA chain and a nucleotide 5′-diphosphate.  The nucleolytic activity is appropriate, as the enzyme is a principal exonuclease component of the RNA-degrading machine known as the degradosome.

But RNA breakdown is not the only enzymatic activity possessed by PNPase.  As I noted in an earlier essay, PNPase was a first (perhaps THE first) nucleotidyltransferase, or RNA polymerase.  Indeed, it was an early candidate for the RNA polymerase (you know, the DNA-dependent RNA polymerases that are responsible for transcription).  This activity reflects the fact that the nucleolytic activity, when reversed, is actually a nucleotidyl transferase activity, in which RNA chains can be extended (in a template-independent fashion) using nucleotide diphosphates as substrates.  The clearest in vivo manifestation of this activity is evident in the many reports that show that PNPase can act as a poly(A) polymerase in vivo [see the review by Slomovic et al. for more on this]; this is true in bacteria and in organelles such as the chloroplast or mitochondria.

Recap

The RNA 2010 Meeting has come and gone.  Previously, in a sort of preview of coming attractions, I gave a list (from the conference web site) of the many invited speakers.  What I thought I would do here is toss out some random comments, to give readers a small taste of the meeting.  (One aside – the abstracts are not “open access” and attendees are asked in the abstract book to not cite anything without authors’ consent.  This means that I won’t be very explicit about the individual talks or posters.  However, in a few instances, I will provide links to related papers.)

Convergent transcription, polyadenylation, RNA editing, and regulation

One of the mechanisms by which polyadenylation may contribute to the regulation of gene expression (on paper, at least) involves gene pairs that are situated near each other and transcribed convergently.  In these instances, polyadenylation and transcription termination need to occur to prevent the production of RNAs that are anti-sense to the two members of the convergently-transcribed gene pair.  Overlapping transcripts could lead to the formation of double-stranded RNAs that could in turn trigger regulatory mechanisms, resulting in altered accumulation of the corresponding transcripts.

It is in this vein that a recent study from Gordon Carmichael’s lab at the University of Connecticut is of interest.  Briefly, these authors report that the early-to-late transition in gene expression in cells infected with the mouse polyoma virus is accomplished (at least in part) by a reduction in polyadenylation efficiency of the primary transcript encoding the so-called late genes.  Interestingly enough, this reduction in polyadenylation efficiency seems to be due to A-to-I editing of the region around the polyadenylation signal.  This editing in turn may be traced to an overlap of the early and late transcripts, such that double-stranded RNAs (the substrate for the A-to-I editing complex) that include the late polyadenylation signal are produced and edited before pre-mRNA processing occurs.

SOC1 and the RNA Underworld

Earlier, I described studies of the so-called SOC1 and FUL genes of Arabidopsis, genes that when mutated in concert change the growth habit of the plant is most remarkable ways.  A report that just came up on Plant Cell Online links one of these genes with one of the mechanisms by which RNAs are turned over in the cell.  Briefly, this study reveals that SOC1 expression is subject to posttranscriptional control, and that this control is linked with a component of the machinery that mediates nonsense-mediated decay (NMD) in plants.  This finding may be of interest for a number of reasons.  One is that NMD hasn’t yet been linked with lots of regulation in plants – it occurs, and we may infer conceptual links between alternative RNA processing and NMD, but much remains to be learned.  A second is that SOC1 functioning, previously implicated in important macroevolutionary transitions in plants, may be altered by many evolutionary processes, including those that affect RNA levels through NMD.

The abstract:

SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1) is regulated by a complex transcriptional regulatory network that allows for the integration of multiple floral regulatory inputs from photoperiods, gibberellin, and FLOWERING LOCUS C. However, the posttranscriptional regulation of SOC1 has not been explored. Here, we report that EARLY FLOWERING9 (ELF9), an Arabidopsis thaliana RNA binding protein, directly targets the SOC1 transcript and reduces SOC1 mRNA levels, possibly through a nonsense-mediated mRNA decay (NMD) mechanism, which leads to the degradation of abnormal transcripts with premature translation termination codons (PTCs). The fully spliced SOC1 transcript is upregulated in elf9 mutants as well as in mutants of NMD core components. Furthermore, a partially spliced SOC1 transcript containing a PTC is upregulated more significantly than the fully spliced transcript in elf9 in an ecotype-dependent manner. A Myc-tagged ELF9 protein (MycELF9) directly binds to the partially spliced SOC1 transcript. Previously known NMD target transcripts of Arabidopsis are also upregulated in elf9 and recognized directly by MycELF9. SOC1 transcript levels are also increased by the inhibition of translational activity of the ribosome. Thus, the SOC1 transcript is one of the direct targets of ELF9, which appears to be involved in NMD-dependent mRNA quality control in Arabidopsis.

The citation (hopefully, I will remember to update it once the paper comes out in print with the updated link for the paper copy):

Hae-Ryong Song, Ju-Dong Song, Jung-Nam Cho, Richard M. Amasino, Bosl Noh,  and Yoo-Sun Noh. The RNA Binding Protein ELF9 Directly Reduces SUPPRESSOR OF OVEREXPRESSION OF CO1 Transcript Levels in Arabidopsis, Possibly via Nonsense-Mediated mRNA Decay.  Plant Cell Advance Online Publication, Published on April 17, 2009; 10.1105/tpc.108.064774

More strangeness …

Awhile ago, I discussed a flurry of papers in Science that showed some curious aspects of transcription and promoters.  It seems as if every passing day brings a new report that pertains to the phenomenon.  A recent issue of Nature brings us two papers, back to back, that are relevant.  The bottom line is that bidirectional transcription is a widespread phenomenon, at least in yeast.  Moreover, this phenomenon is responsible, not just for divergent transcription of mRNA-encoding genes, but also for the production of so-called Cryptic Unstable Transcripts and other uncharacterized RNAs.  The abstracts and some brief commentary are beneath the fold.

Interesting stuff

While my yard is recovering from the ice, and I from today’s UK game, I thought I would toss out a few interesting abstracts that touch on important and contentious issues.  Peek beneath the fold and, as always, enjoy.

Strange things at promoters

A group of interesting papers popped up on ScienceExpress this past week.  These papers (by Core et al., Seila et al., He et al., and Preker et al.) all describe characterizations of unusual patterns of transcription in human cells.  The bottom line (well, one bottom line – there are lots of interesting data in these studies, and the nuances may take readers in slightly different directions) is that, for numerous promoters, transcription extends in both directions, not just in the one direction that is usually associated with productive (= leading to synthesis of a processed and translated mRNA) transcription.  Moreover, this bidirectional transcription is quite distinct from that associated productive transcription, in that it yields short and relatively unstable RNAs.  More elaboration follows below the fold.  As always, enjoy.

Off with their heads!

As noted in this earlier essay, the poly(A) tail collaborates with the 5′-end of the mRNA (the so-called cap) to promote both mRNA translation and stability.  Accordingly, decapping is a good hallmark for mRNA turnover.  In a recent issue of The Plant Cell, Jiao et al. describe an approach to study uncapped mRNAs on a global basis.  Briefly, these authors take advantage of the fact that an uncapped mRNA has a 5′ phosphate group, and thus can be a substrate for RNA ligase.  By attaching an RNA adapter to the uncapped mRNAs using this enzyme, and then purifying and amplifying DNA products derived from these, the authors were able to prepare probes for microarray studies.  Thus, they were able to assess uncapped mRNA abundance on a genome-wide basis.  As a test for this approach, they studied decapping genome-wide during the early stages of flowering using a mutant arrested for flower development at a specific stage, but carrying a chemically-inducible transgene that could trigger flowering by providing for some of the functionality missing in the mutant.  This group found that a sizable portion of mRNAs that could be detected on the microarrays (approaching 40%) were either “over-capped” or “under-capped”; that is to say, the relative abundances of uncapped mRNAs differed from the total levels of the corresponding transcripts.  They also found a number of transcripts (some 300 or so) whose capping status changed during flowering.  All told, as stated by the authors, this system should be useful for exploring regulated mRNA turnover, and for identifying correlations between mRNA sequence/structure and stability.