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RNA-BINDING PROTEINS IN FUNGI AND THEIR ROLE IN mRNA LOCALIZATION

.*

* Helmholtz Zentrum München, Institute for Structural Biology and Gene Center of the Munich University, Munich, Germany Email: ed.nehcneum-ztlohmleh@gnissein

RNA Binding Proteins edited by Lorkovic Zdravko.
©2011 Landes Bioscience and Springer Science+Business Media.
Read this chapter in the Madame Curie Bioscience Database here.

mRNA localization is a widely used mechanism for the spatial and temporal control of gene expression. In higher eukaryotes, the mRNA-transport machinery has a complexity that renders a mechanistic understanding at the molecular level difficult. During the last 15 years, studies in fungi have proven to be attractive alternatives. They are experimentally more accessible and the organization of their mRNA-transport particles is less complex. Here, our current understanding of mRNA transport in fungi will be summarized. The highly specific mRNA localization observed in the budding yeast Saccharomyces cerevisiae will be compared with mRNA localization in the human pathogen Candida albicans and the less specific transport of transcripts in the plant pathogen Ustilago maydis.

INTRODUCTION

One of the great advantages of yeast is its simplicity. Although being a eukaryotic organism, its cellular machinery often relies on fewer factors and less complex regulation. Based on our current knowledge, also mRNA localization appears to follow this rule. Whereas this process is found in virtually all eukaryotes, the number of proteins required to assemble a functional mRNA-transport complex appears to be considerably lower. A second important advantage is the comparably small size of yeast genomes, which can be easily manipulated and challenged by genetic screens.

For these reasons, it is not entirely surprising that the most comprehensively understood event of mRNA localization is found in the budding yeast S. cerevisiae.1

In this chapter, we will first outline our current understanding of how RNA-binding proteins contribute in different ways to mRNA localization in the budding yeast (Fig. 1A). Since mRNA localization has also been described in other fungi, we will continue with a description of mRNA localization in the human pathogen Candida albicans (Fig. 1B,C) and the transport of transcripts in the plant pathogen Ustilago maydis (Fig. 1D). A summary of RNA-binding proteins implicated in directional mRNA transport in these fungi is provided in Table 1.

Figure 1. Images of mRNA localization in different fungi.

Figure 1

Images of mRNA localization in different fungi. A) In budding yeast Saccharomyces cerevisiae the ASH1 mRNA is localized in the daughter cell. B) In the filamentous fungus Candida albicans the ASH1 mRNA is localized to the hyphal tip by a machinery that (more...)

Table 1. Summary of RNA-binding proteins required for mRNA localization in yeast.

Table 1

Summary of RNA-binding proteins required for mRNA localization in yeast.

OVERVIEW OF mRNAs LOCALIZATION IN S. CEREVISIAE

During mitosis, S. cerevisiae undergoes unequal cell division, resulting in a larger mother cell and a smaller daughter cell.2 Whereas the mother cell undergoes a genomic recombination in the MAT gene locus (from a to a or vice versa), the daughter cell remains unchanged. This genomic recombination is mediated by the enzymatic activity of the HO endonuclease.2 It ensures that both cells adopt different identities after cytokinesis and thus guarantees an equal distribution of mating types in a population.

About 15 years ago, it was reported that the localization of ASH1 mRNA in the daughter cell and its local translation mediates the selective inhibition of mating-type switching in the daughter cell.3,4 Its protein product Ash1p suppresses the HO endonuclease and therefore inhibits mating-type switching in the daughter cell.2 A genetic screen identified the main players of this process,5 which were referred to as SHE proteins. In the following years, work from several research groups helped to clarify their roles in mRNA localization.1,6 Since then, more than 30 additional transcripts have been shown to be transported by the SHE machinery into the daughter cell.7-10

The molecular motor providing the motile activity for daughter cell localization of mRNAs is the type V myosin She1p.5 It is commonly referred to as Myo4p and moves its cargo along actin filaments (Fig. 2). A myosin adapter, termed She3p, directly binds with its N-terminal half to the tail of Myo4p.11-14 Both proteins form a constitutive cytoplasmic cocomplex. In addition, the C-terminus of She3p interacts with the RNA-binding protein She2p.11,15

Figure 2.. Schematic drawing of ASH1 mRNA localization in the budding yeast S.

Figure 2.

Schematic drawing of ASH1 mRNA localization in the budding yeast S. cerevisiae. In the nucleus of the mother cell (dashed box left) ASH1 mRNA interacts with She2p cotranscriptionally. The complex is joined by Puf6p and Khd1p, passes through the nucleolus (more...)

She2p is an unusual RNA-binding protein16,17 that shuttles into the nucleus and is exported together with the ASH1 mRNA into the cytoplasm (Fig. 2).18-21 On its way out of the nucleus, the ASH1 complex passes through the nucleolus.18

After export, the She2p-RNA complex interacts with the C-terminal half of She3p to form a larger, motor-containing complex.11,15,22 Recent single-particle experiments with in vivo-purified transport particles demonstrated that this minimal complex, consisting of Myo4p, She3p, She2p, and RNA, indeed constitutes a motile mRNP.23

However, for efficient mRNA localization in vivo additional RNA-binding proteins are required (Table 1). Two of these accessory factors, termed Puf6p and Khd1p, are involved in translational repression during transport and de-repression at the site of localization (Fig. 2).24,25 Both translational receptors seem to associate with distinct subsets of localizing mRNAs.24-28 Like She2p, Puf6p and Khd1p shuttle into the nucleus and are most likely exported together with ASH1 mRNA into the cytoplasm.18,21

The third accessory factor is Loc1p.29 Although this protein was discovered before Puf6p and Khd1p, it remains to be the most mysterious one. Loc1p shows strictly nucleolar localization and is therefore not directly involved in cytoplasmic events (Fig. 2).29 Nevertheless, deletion of loc1 results in defective ASH1 mRNA localization in the cytoplasm.29 To date, we fail to understand why.

In addition to mRNA transport, concomitant inheritance of cortical endoplasmic reticulum (ER) by the SHE machinery has been reported.12 For this process, Myo4p and She3p but not She2p are required. Nevertheless, She2p and ASH1 mRNA directly associate with ER membranes.30 It might be that this association and comigration with ER constitutes an independent and alternative path for mRNA localization. However, since we still fail to understand this interaction and its precise meaning for ASH1 localization, aspect of ER inheritance will not be explained here further.

In the following paragraphs, we will rather discuss in more details how the above-mentioned RNA-binding proteins interact and participate to mediate directional mRNA transport. Details on the function of the myosin motor can be found elsewhere13,14,31-33 and will not be covered by this chapter.

BUD-LOCALIZING mRNAs

In addition to ASH1 mRNA, She2p binding to more than 30 transcripts has been reported, of which about half clearly localize in a She2p-dependent manner.7-10 Localizing mRNAs contain at least one cis-acting element, to which She2p binds. Such cis-acting localization elements are also known as zip-code elements34 and usually adopt stem-loop structures.35,36 A recent study used double fluorescence in situ hybridization (FISH) to show that transport particles contain combinations of different mRNA species that are transported together.37

Attempts to find common features for all of these zip-code elements failed so far, but for several well-defined zip-code elements a stem-loop structure is necessary for binding.11,38-40 In a three-hybrid assay Pascal Chartrand and colleagues identified sequence motifs in a subset of zip-code elements that are required for She2p binding.36 The identified motif consists of a CGA base triplet located in a loop and a single cytosine in a second loop. Both loops are separated by a double-stranded RNA helix of defined length. In a study by Joseph DeRisi and colleagues again a three-hybrid screen was used to demonstrate that this base triplet may not be sufficient for binding and that the cytosine may be dispensible.41 It seems obvious that further functional and structural studies with different RNA-zip-code elements are necessary to understand the features of zip code RNAs that are recognized by the transport machinery.

Interestingly, it has been noted that several of the She2p-dependent mRNAs also have a functional relationship. Almost half of the She2p-dependently localizing mRNAs encode for membrane-associated proteins.9

THE CORE RNA-BINDING PROTEIN She2p

She2p has long been considered to be the only RNA-binding protein required for the specific recognition of transcripts and their incorporation into transport particles.1,6,42 This picture only changed recently, when She3p was identified as a novel, cytoplasmic RNA-binding protein that acts in concert with She2p to recognize localizing mRNAs (see below).22

She2p shuttles into the nucleus with the help of the importin-alpha Srp1p.19,21 There, She2p is located at nuclear foci, which are probably sites of ASH1 transcription.18 Recent chromatin-immunoprecipitation (ChIP) studies confirmed that She2p is indeed recruited to sites of active transcription, albeit with no preference for genes encoding localizing transcripts (Fig. 2).22,43 This recruitment depends on the transcriptional elongation factors Spt4 and Spt543 and does not require RNA-binding.22,43 From these findings a model has been suggested in which localizing transcripts are cotranscriptionally loaded with She2p.43 Because it still remains unclear when and how specific She2p binds to localizing transcripts in the nucleus, additional studies will have to clarify the mechanistic details of these early events.

Once the mRNA has been synthesized, it passes through the nucleolus.18,21 Here, the ASH1 complex associates with the nucleolar protein Loc1p, for reasons still unknown. It is clear, however, that Loc1p does not enter the cytoplasm and thus only indirectly influences the cytoplasmic fate of ASH1 mRNA.29 After nuclear export, the pre-mRNP matures into an active, motor-containing particle (Fig. 2). The key interaction for this maturation is the formation of the ternary complex between She2p, She3p and localizing RNA.22 Here, both proteins bind to the RNA and to each other. In that way, they act synergistically to achieve high binding specificity and affinity.22 Because She3p is constitutively associated with the motor Myo4p already before this event, the ternary complex formation brings together the RNA and the motor. In summary this cytoplasmic assembly event constitutes a key quality control step for the selective transport of mRNAs with zip-code elements (Fig. 2).

Determination of the crystal structure of She2p brought the surprising finding that it consists of an unusual type of nucleic-acid binding domain.17 Whereas the crystal structure revealed a homo-dimeric protein,17 its analysis in solution revealed a tetrameric assembly of two dimers in a head-to-head interaction (Fig. 3A).16,23 Disruption of She2p tetramer formation results in reduced RNA binding and impaired mRNA localization in vivo.16 One of the most striking features of this tetramer is the four small helices that protrude at right angles from the body of the structure into the solvent (Fig. 3A). These helices are required for the interaction with She3p, for RNA binding, and thus for specific recognition of localizing RNAs.22 The distance between two alpha-helices on one side of the structure is large enough to accommodate up to two double-stranded RNA molecules side-by-side.16 In addition, the continuous surface between the two helices has been shown to be involved in RNA binding.17 Thus the structural analysis indicates that the She2p tetramer is well suited for specific RNA recognition.

Figure 3.. The core RNA-binding proteins of the ASH1 mRNA transport complex from S.

Figure 3.

The core RNA-binding proteins of the ASH1 mRNA transport complex from S. cerevisiae. A) Structural model of the She2p tetramer, as derived from X-ray crystallographic and small angle X-ray scattering (SAXS) analyses., Regions highlighted in red (online (more...)

The more surprising it was to find that RNA binding of She2p alone has a rather low specificity.16,18,22 This observation suggested that in vivo additional features must contribute to achieve the highly specific transport of mRNAs observed in cells. The discovery of the RNA-binding properties of She3p and its synergistic binding with She2p (see next paragraph) offered this missing piece in the puzzle.22

THE MYOSIN ADAPTER AND RNA-BINDING PROTEIN She3p

She3p has been identified by yeast-two-hybrid screens and co-immunoprecipitation experiments as a direct interactor of She2p and of the myosin motor Myo4p.11,15,19,44 For a long time it was believed that She3p only acts as a linker between the RNA-binding protein She2p and the motor Myo4p.1,6,31,32,42 Consistent with this assumption is that relatively tight binding was measured for the Myo4p-She3p interaction.13 However, the interaction between She2p and She3p in absence of RNA was measured to be far too weak for a complex formation in vivo.22 Instead, in vitro reconstitution experiments with recombinant proteins demonstrated that She3p is an RNA binding protein with rather low specificity. It has to interact with She2p to form a tight and specific ternary complex with localizing RNAs (Fig. 2).22 Thus, tight She3p binding to She2p depends on the simultaneous interaction of both proteins with mRNA. This specific RNA recognition is only achieved during the late assembly of the mature transport complex in the cytoplasm (Fig. 2).

Within the 425 amino acid long protein sequence of She3p, a sub-fragment of 92 residues is sufficient for RNA binding and for synergistic interaction with She2p (Fig. 3B). Surprisingly, database searches with the protein sequence of She3p fail to yield any significant similarity to known RNA- or DNA-binding domains. It suggests that She3p might bind RNA and She2p via an unusual structural arrangement.

In certain yeast species like C. albicans a She3p homolog but not a She2p homolog is present in the genome (Fig. 3C).22,45 From this, the interesting question arises whether such species also actively localize mRNAs. Indeed, C. albicans transports mRNAs in an She3p-dependent manner (for details, see below).45 It suggests that C. albicans either uses a different She3p-binding partner than She2p or that She3p achieves higher RNA-binding specificity on its own. It will be interesting to see which of these options nature has chosen to ensure specific mRNA transport in these species.

THE TRANSLATIONAL REPRESSOR Puf6p

Like She2p, the Puf6p protein shuttles between the cytoplasm and nucleus.21 Puf6p binds to zip-code elements in the ASH1 mRNA and represses translation during mRNA transport.24,26

Puf6p mainly consists of seven Pumilio-like repeats,26 which are typical for Pumilio-family proteins.46 This family of proteins usually have multiple Pumilio-like repeats that stack onto each other to produce an elongated structure.47 These elongated, often banana-like structures bind to RNAs via their concave inner surface. Because of its pronounced homology to Pumilio-like proteins with known structures, it can be assumed that Puf6p adopts a similar shape and binds RNA in a comparable manner.

Since Puf6p could be co-immunoprecipitated with She2p from yeast extracts even after RNase digestion, a direct interaction between both proteins had been suggested.21 Binding studies with recombinant proteins, however, failed to confirm such a direct interaction.22 Therefore the in vitro results rather imply that ASH1 mRNPs purified from extracts are inert enough to resist RNase treatment. Interestingly, the binding site of Puf6p on the ASH1 mRNA is very close to a She2p binding site.26 This vicinity of both factors could potentially help to facilitate the formation of such inert complexes.

After Puf6p has joined the nuclear complex, it shuttles with the localizing mRNAs into the cytoplasm (Fig. 2). There Puf6p acts as an associated factor while being dispensable for the formation of core motile particles.23 In this function, Puf6p mediates the translational repression to prevent premature translation of ASH1 mRNA during its transport to the daughter cell.24 Upon Puf6p deletion, premature translation in the mother cell results in reduced bud-tip localization of ASH1 mRNA and defective mating-type switching.24,26 The mechanism of Puf6p-mediated translational repression has recently been solved: Puf6p interacts with the general translation factor eIF5B to prevent translation initiation of its bound transcripts.24 Interestingly, this interaction is RNA-dependent. The translational repression is released by phosphorylation of Puf6p by the casein kinase II, most likely at the bud tip.24

THE TRANSLATIONAL REPRESSOR Khd1p

Khd1p was identified by a systematic assessment of RNA-binding proteins to be required for efficient ASH1 mRNA localization.28 The genetic inactivation of Khd1 results in a reduction but not a complete loss of ASH1 mRNA localization.28

This reduced localization is rather similar to the defect observed when Puf6p is inactivated.26 Also the functions of Puf6p and Khd1p are comparable: Khd1p also acts as a translational repressor during mRNA transport, albeit by a different mechanism,25 and both proteins shuttle between the nucleus and the cytoplasm.18,21 Furthermore, unlike She2p but similar to Puf6p, Khd1p only binds to a single RNA region at the beginning of the open reading frame of ASH1 mRNA.27,28 It seems likely that Khd1p and Puf6p have redundant functions in translational repression. Alternatively, these proteins might complement each other by repressing the translation of different subsets of localizing mRNAs.

Khd1p contains three so-called K-homology (KH) domains. The KH domains are highly conserved and abundant RNA binding domains.47,48 It suggests that Khd1p binds localizing RNAs through these domains. Khd1p also interacts with the general translation initiation factor eIF4G1. This interaction results in the inhibition of premature ASH1 mRNA translation during its transport to the bud cell.25 At the bud tip, Khd1p becomes phosphorylated by the membrane-associated kinase Yck1p.25 Phosphorylation reduces the affinity of Khd1p for ASH1 mRNA and releases the transcripts for local translation at the bud tip.

Interestingly, micro-array analysis of RNA-binding partners of Khd1p shows that this protein interacts with a large range of transcripts including only a subset of bud-localizing mRNAs.27 A similar study for Puf6p is still missing. Further work will be required to understand the specificities and complementarity of these two translational repressors.

THE NUCLEOLAR RNA-BINDING PROTEIN Loc1p

Loc1p has been identified in a three-hybrid screen to bind to ASH1 mRNA.29 This protein is strictly localized in the nucleus,29 with a sub-localization to the nucleolus.18,49 Since the nucleolus is well-known as site of ribosome biogenesis,50 it was surprising to discover that deletion of Loc1p results in a reduction of cytoplasmic localization of ASH1 mRNA.29 The second, more expected defect observed in a loc1 mutant is impaired biogenesis of the large ribosomal subunit.49 In loc1Δ cells, 35S pre-rRNA accumulates, 25S r-RNA is decreased, and 60S ribosomal subunits are not efficiently exported into the cytoplasm. Since deletion of loc1 results in a two-fold increase of Ash1p but not of Actin levels, it has been suggested that Loc1p is involved in the regulation of ASH1 mRNA translation.51 An apparent uncertainty with this reasoning is that impairing ribosome biogenesis might influence translation of transcripts in an unpredictable manner and that the observed increase in Ash1p translation could still be a rather unspecific effect.

Co-immunoprecipitation experiments showed that Loc1p interacts with She2p in an RNase-independent manner.21 This observation suggests that both proteins are part of the same protein complex or even bind directly to each other. Again, the mechanistic implications of this interaction remain to be elucidated. Attempts to identify known protein domains or even to predict the three-dimensional fold of Loc1p failed. Thus, also from a structural biology point of view, no hints can be derived on its precise molecular function.

In summary, Loc1p is involved in two seemingly unrelated, but RNA-dependent processes. It remains to be seen whether Loc1p acts more as a general factor or if it is involved in these two tasks with a very specific mission.

LONG-DISTANCE TRANSPORT OF mRNAs IN THE FILAMENTOUS FUNGUS CANDIDA ALBICANS

The filamentous fungus Candida albicans is an opportunistic human pathogen that causes infections in immune-compromised patients.52 It exists in different morphological forms.53 In particular, the hyphal form has been associated with virulescence. Already a while ago, a study suggested that directional RNA transport may also take place in C. albicans. Ralf-Peter Jansen and colleagues had introduced ASH1 mRNA from C. albicans into S. cerevisiae and observed its accumulation in the daughter cell.44

A more recent study found that C. albicans has a homolog of She3p but not of She2p.45 Alexander Johnson and colleagues used a combination of genetic manipulation and biochemical experiments to show that there is indeed She3p-dependent transport of mRNAs in C. albicans (Fig. 4):45 First, they observed ASH1 mRNA localization in the tip cell of hyphae (Fig. 1B). Second, genetic deletion of both she3 alleles resulted in loss of the tip localization of ASH1 mRNA and impaired filamentous growth (Fig. 1C). Third, copurification of mRNAs with She3p yielded a distinct set of about 40 transcripts, a part of which does localize in a She3p-dependent manner. Amongst them only a fraction, including ASH1 mRNA, have clear homologs to localizing mRNAs in S. cerevisiae.45

Figure 4.. Schematic drawing of mRNA localization in C.

Figure 4.

Schematic drawing of mRNA localization in C. albicans. ASH1 mRNA and other transcripts are transported along microtubules to the hyphal tip. At the tip, Ash1p is produced by local translation. Besides ASH1 mRNA, the RNA-binding protein and myosin adapter (more...)

Obviously many questions remain regarding the identity and function of the components of the She3p-dependent transport complex in C. albicans. For instance, how does C. albicans substitute the function of She2p known from S. cerevisiae? Interestingly, C. albicans not only lacks She2p but also fails to have a Myo4p homolog.45 In S. cerevisiae Myo4p is required to move ASH1 mRNPs into the bud cell.5 Instead, C. albicans only has a homolog of Myo2p,45 which has not been reported to play a role in ASH1 transport in S. cerevisiae. So another interesting question is which motor protein provides the motile activity for active transport. It will be very interesting to see how flexible evolution has handled the function of these proteins to achieve directional mRNA transport.

LONG-DISTANCE TRANSPORT OF mRNAs IN THE FILAMENTOUS FUNGUS USTILAGO MAYDIS

Also the corn pathogen Ustilago maydis is a filamentous fungus that relies on active transport processes to achieve hyphal growth.54 Like in S. cerevisiae, also U. maydis actively transports mRNAs along the cytoskeleton (Fig. 5), albeit with marked differences. In contrast to S. cerevisiae, not all molecular players are known yet. One central RNA-binding protein, termed Rrm4, has been shown to be required for directional mRNA transport. Rrm4-containing particles move with high processivity to both poles.55 Surprisingly, these particles do not become anchored at the tip, but rather turn around and move backwards in a retrograde manner. Deletion of Rrm4 results in defects in filamentous growth as well as in reduced virulence.56

Figure 5.. Schematic drawing of mRNA transport in U.

Figure 5.

Schematic drawing of mRNA transport in U. maydis. The RNA-binding protein Rrm4 and the poly-A binding protein (PABP) are both colocalizing in transport particles. Rrm4 binds to CA-rich elements in the transported mRNAs and most likely tethers them to (more...)

Rrm4 contains three N-terminal RNA recognition motifs (RRMs) and one C-terminal PABC (poly-A binding protein C-terminus) domain. RRMs are highly conserved and widespread RNA-binding domains,57 whereas the PABC domain has been shown in humans to be responsible for protein interaction with the poly-A binding protein.58,59 Deletion of the first RRM results in a loss of function, indicating that RNA-binding is important for Rrm4 function.55 Also mutations in the PABC domain result in defects similar to the inactivation of the entire Rrm4 protein.55 It suggests that Rrm4 might interact with the poly-A binding protein (PABP). Indeed, the PABP of U. maydis (PAB1) colocalizes with Rrm4 in virtually all shuttling particles.60

By in vivo UV cross-linking and immunoprecipitation (CLIP) experiments,61 about 50 transcripts were identified to interact with Rrm4.60 These RNAs encode for proteins involved in translation, cell fate and cell polarity. Most of them contain regions with a bias towards CA-rich motifs, suggesting that Rrm4 binds preferentially to elements with a CA bias.60

CONCLUSION

Given our lack of knowledge on many molecular details of mRNA transport in C. albicans and U. maydis, it seems difficult to directly compare these species. There are, however, obvious differences. For instance the transport in U. maydis occurs along microtubules, whereas ASH1 mRNA transport in S. cerevisiae and possibly also in C. albicans proceeds along actin filaments. Due to the filamentous nature of U. maydis and of C. albicans the mRNA transport occurs over much longer distances than in S. cerevisiae. If mRNA localization in C. albicans indeed proceeds along actin filaments, it would mean that the often-made assumption "short distance transport follows actin filaments—long distance transport occurs along microtubules" does not hold true in all cases. Also when we compare the RNA-binding proteins and domains that are utilized in the apparently unrelated mRNA-transport processes of S. cerevisiae and U. maydis, we find little overlap. Thus, studies in fungi suggest that there is not a single, general principle for all transport events. There might be universal principles though which remain to be discovered by future mechanistic studies.

Another very interesting issue is specificity of mRNA recognition for transport. In U. maydis mRNA transport appears to be less efficient and potentially also less specific than in S. cerevisiae. Why this difference? A likely explanation is their different functional requirements. In S. cerevisiae the goal is to efficiently deplete the mother cell from ASH1 transcripts. Already mild defects in ASH1 mRNA localization result in disrupted regulation of mating-type switching. For this reason, ASH1 mRNA localization has to be very efficient. In the long, filamentous fungus U. maydis, however, active transport appears to be in place to overcome limitations in diffusion. Due to the long extensions of a cell, diffusion is not sufficient to guarantee even distribution of mRNAs and other molecules. To overcome this problem, U. maydis appears to use active transport.

The more details we learn about the molecular machines in these species, the better we will be able to comprehend if, despite molecular differences, there are universal principles that can be found in all of them. However, we may also find principles that only apply to distinct subsets of cellular tasks.

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