Monthly Archives: September 2012

The CSR-1 siRNA pathway gets more enigmatic

A recent paper forces a reappraisal of the role of CSR-1 its associated 22G-RNAs, and demonstrates a positive regulatory role for this RNAi pathway in C. elegans.

As described in a previous post, depletion of the Argonaute protein CSR-1, or the proteins responsible for the biogenesis of the endo-siRNAs with which its complexes (the RdRP EGO-1, and the helicase DRH-3), results in defective mitotic chromosome segregation and sterility. To explain these findings Claycomb et al. proposed that the CSR-1 22G-RNA pathway acted to organise the proper compaction of the holocentric chromosomes of C. elegans, and the assembly of the kinetochores necessary for their proper segregation. (I strongly recommend reading the earlier post describing this paper’s findings).

Claycomb et al. had found that expression of most genes targeted by CSR-1 associated 22G-RNAs was not significantly altered in csr-1 mutants. Avgousti et al. went back over the same data and found that, although this was true in the main, expression of most of the genes encoding histone proteins was downregulated in csr-1 mutants. It had previously been shown that downregulation of just one histone gene could cause chromosome segregation and sterility phenotypes in worms. This lead Avgousti et al. to hypothesise that the defects seen in csr-1, ego-1 and drh-3 mutants may be caused by defective histone production, rather than the model proposed by Claycomb et al.

Histone proteins make up the core of the nucleosome and are multiply encoded in all eukaryotic genomes. Histone mRNAs are processed in a special way; generally their 3’UTRs are not polyadenylated; instead, downstream of a conserved stem-loop structure, a histone specific sequence (HDE) is recognised and cleaved by the U7 snRNA (an important splicing factor). Both HDE sequences and the U7 snRNA are not present in C. elegans. Avgousti et al therefore tested whether this key histone mRNA processing stage was instead being mediated by CSR-1 and its associated endo-siRNAs in worms.

Using a synthetic oligonucleotide identical to the region of the 3’UTR downstream of the stem-loop from the histone 2A pre-mRNA, they demonstrated that CSR-1 directly binds histone mRNAs. This binding was abrogated upon RNAi depletion of the RdRP EGO-1, showing that CSR-1 binding was dependent on the 22G-RNAs generated by EGO-1. Avgousti et al. also demonstrated that upon knockdown of CSR-1 or EGO-1, or in drh-3 mutants, unprocessed histone pre-mRNAs accumulate, whilst processed histone mRNAs and proteins are depleted.

The strongest evidence supporting the hypothesis that defective histone mRNA processing causes the defects seen in csr-1 mutants was a series of transgenic rescue experiments. Histone overexpression from transgenes, designed to not require 3’UTR mRNA cleavage, was able to counteract the effects of csr-1 or ego-1 RNAi knockdown, whereas transgenes that did required 3’UTR processing could not.

It seems likely therefore that in C. elegans the 3’UTR cleavage of histone pre-mRNAs is performed by CSR-1/22G-RNA complexes. CSR-1 has been shown to possess endonuclease ‘slicer’ activity, but although a likely candidate, it is too early to say whether it directly performs the cleavage or recruits other factors to perform the reaction. I think this paper blows a large hole in the model proposed by Claycomb et al. to explain the role of CSR-1 22G-RNAs; suggesting that the observed chromosome segregation defects are indirectly caused by a failure to produce adequate histones, rather than a failure to direct the organisation of mitotic chromosomes. However, the hypothesis certainly requires further and more subtle experiments. The paper also further muddies the waters on the question of just what the CSR-1 22G-RNA system is doing in most cases. The recognition of histone mRNA 3’UTRs can only account for a very small proportion of this endo-siRNA population. As discussed in other posts the CSR-1 22G-RNA system is the prime candidate to be an epigenetic licensing anti-silencing pathway. Do the two different CSR-1 isoforms perform two different functions; one licensing transcription and the other replacing the U7 snRNA splicing apparatus? Is this pre-mRNA splicing role confined to histone mRNAs? An important first of this paper is the demonstration of a positive role in regulating gene expression for an RNAi system. Generally, the various RNAi pathways negatively regulate gene expression; either resulting in slicing and degradation of transcripts, directing silencing chromatin modifications etc. In this case mRNA processing by the CSR-1 endo-siRNA system leads to proper expression of histones at key periods of rapid cell division (eg. early embryogenesis). Personally, I’m looking forward to more contentious interpretations of this pathway from the research groups involved!

Avgousti DC, Palani S, Sherman Y, & Grishok A (2012). CSR-1 RNAi pathway positively regulates histone expression in C. elegans. The EMBO journal PMID: 22863779

Claycomb JM, Batista PJ, Pang KM, Gu W, Vasale JJ, van Wolfswinkel JC, Chaves DA, Shirayama M, Mitani S, Ketting RF, Conte D Jr, & Mello CC (2009). The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell, 139 (1), 123-34 PMID: 19804758

Chromosomal Flip-Flop

A study describes how phenotypic switching in Staphylococcus aureus is caused by a reversible large-scale genomic inversion.

Clonal bacterial populations often display various phenotypes. This diversity is most obviously identifiable as colony variation. Many different bacterial genera display ‘small colony variants’ (SCVs), the occurrence of which is generally attributable to deficiencies in various metabolic pathways.

Cui et al have characterised an STV strain of Staphylococcus aureus which reverts to a normal colony variant (NCV) at a frequency of 1-3 in a 1000. Interestingly the NCV progeny revert back to SCV in 1-10% of cases. This frequent bi-directional reversion was stably maintained at these ratios; homogeneous colony populations could never be isolated.

The small colony variant displayed some important phenotypic differences to the NCV. As well as slow growth and less pigmentation, it was susceptible to β-lactam antibiotics whilst the NCV was not. The authors identified over a hundred genes were differentially expressed between the two variants, and that their susceptibilities to many chemicals were different.

Diagram showing reversible genomic inversion forms caused by homologous recombination at inverted repeat regions (break points. BPs)

When Cui et al. sequenced the genomes of the two variants, they discovered that nearly half of the genome (1.26 Mb of 2.87 Mb) was differenttly aligned. This ‘X-shaped’ chromosome inversion occurred between two oppositely oriented pathogenicity islands, symmetrically opposite each other on the chromosome with respect to the replication axis. Each pathogenicity island contained two copies of an identical 3,638bp long sequence. It appears that homologous recombination can occur at these sites and generate the genomic inversion. This is in agreement with experiments in which the authors altered levels of the key recombination regulatory protein RecA; finding that they could increase the rate of reversion with higher recA expression.

The chromosomal flip-flopping therefore regulates the maintenance of two different S. aureus phenotypic variants. The two forms have different advantages and disadvantages. The original SCV strain isolated from a patient suffering persistent reinfection of a surgical site. It appears that the SCV may facilitate immune evasion, whilst the NCV has higher antibiotic resistance. Maintaining a balance between the two variants within the S. aureus population therefore functions as an evolutionarily useful bet-hedging strategy.

This type of flexible genome organisation serving as a self-organising regulatory mechanism for the maintenance of a bi-stable heterogeneous cell population may well be a more wide-spread bacterial evolutionary strategy.

Cui L, Neoh HM, Iwamoto A, & Hiramatsu K (2012). Coordinated phenotype switching with large-scale chromosome flip-flop inversion observed in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 109 (25) PMID: 22645353

Expanding the Conjugative Realm

A recent paper demonstrates that a broader range of plasmids can be transferred by conjugation than previously thought.

Integrative and conjugative elements (ICEs, aka conjugative transposons) are a variety of bacterial mobile element generally found integrated into the host genome, but capable of excision and transfer to other cells via conjugation. I’ve previously written a short review of some of their key features, which may serve as a helpful introduction to this post. As well as transferring themselves between cells, ICEs and conjugative plasmids can mobilise other DNA elements, such as integrative mobilizable elements (IMEs) and mobilizable plasmids, that aren’t independently capable of self-transfer.

The conjugative transfer of any of these elements generally rests upon the generation of a single-stranded DNA molecule from the circular dsDNA mobile genetic element. The ssDNA is formed by a mobilising relaxase (Mob) nicking the circular DNA at an origin of transfer (oriT) sequence, followed by the unwinding of the strands by a host-derived helicase. Mob covalently binds the nicked end forming the ‘relaxosome’. A coupling protein is responsible for targeting the relaxosome to the conjugative apparatus (a type 4 secretion system, T4SS).

Plasmids that are incapable of self-transfer, but can be mobilised in trans by conjugative elements, generally encode their own mobilising relaxase and a cognate oriT site. These functions are separate from their replication system, which does however consist of similar components; a replication relaxase (Rep) which nicks and binds to an origin of replication (ori).

Lee et al. have discovered that three plasmids, which had been classified as non-mobilisable due to their lack of Mob/oriT functions, can in fact be transferred between Bacillus subtilis cells by the conjugation system of an ICE, ICEBs1. The three plasmids’ (pC194, pBS42, and pHP13) transfer required the conjugation machinery and coupling enzyme (ConQ) of ICEBs1, but was not dependent on it’s relaxase (NicK). Transfer could occur concomitantly with that of ICEBs1 or in it’s absence; showing that transfer did not act in cis due to integration of the plasmid into ICEBs1.

The authors found that, in the case of pBS42, it’s replicative relaxase was necessary for mobilisation. They therefore think it likely that in all three cases the Rep/ori system is also capable of mediating mobilisation functions. This blurring of the distinctions between Rep/ori and Mob/oriT systems has important ramifications. It opens up the possibility that many rolling-circle replicating plasmids that had been classed as non-mobilisable can in fact be transferred between cells via conjugation.

From an evolutionary perspective, these findings are important for understanding the persistence of plasmids in bacterial populations. Non-mobilisable plasmids would only be maintained in the population because benefits conferred on their hosts. If however many more ‘non-mobilisable’ plasmids can be disseminated by horizontal transfer, their persistence can be better explained. This study therefore expands the importance of conjugation in understanding bacterial evolution. Future studies will need to analyse the extent of interactions between coupling proteins and replication relaxases to better gauge the trans-mobilisation of genetic elements, and re-classify the mobility status of many plasmids.

Lee CA, Thomas J, & Grossman AD (2012). The Bacillus subtilis conjugative transposon ICEBs1 mobilizes plasmids lacking dedicated mobilization functions. Journal of bacteriology, 194 (12), 3165-72 PMID: 22505685

Epigenetic Licensing of a Sex Determination Gene

A recent series of papers describing interacting small RNA pathways in C. elegans, posited the existence of an anti-silencing pathway responsible for licensing the expression of germline transcripts. Johnson and Spence (Science. 2011) published the first paper suggesting such a pathway. Using an elegant series of genetic experiments, they found that maternally supplied RNA of the sex determination gene fem-1 was necessary for normal zygotic fem-1 activity. In the absence of this maternal component, normal fem-1 alleles are epigenetically silenced.

In C. elegans, sex is determined by the ratio of sex chromosomes to autosomes. Worms with one X chromosome become males, whilst those with two develop as self-fertile hermaphrodites. Mutations in genes in the sex determination pathway can give rise to true females. For instance, fem-1 is required for masculinization in both males and hermaphrodites; worms deficient for both maternal and zygotic fem-1 activity lack all male development.

Johnson and Spence noticed some discrepancies between the relative importance of the maternal and zygotic components of fem-1 action. Homozygous fem-1 mutants, born of heterozygous mothers show partial male development because of maternally supplied fem-1. Zygotically heterozygous progeny of female worms homozygous for point mutations in fem-1 are phenotypically normal; that is to say that despite the lack of any maternally derived active FEM-1 protein, male development can proceed normally. However, similar crosses, in which fem-1 deletion alleles are used rather than point mutations, give rise to heterozygous worms showing feminization of the germ line (Fog phenotypes). To prove the requirement of a maternal fem-1 product for spermatogenesis, Johnson and Spence performed a clever genetic trick that produced worms that were homozygous for the wild-type fem-1 allele but were born of a mother homozygous for the deletion mutation. Most of these worms also exhibited Fog phenotypes. Other strong loss of function alleles that eliminated FEM-1 protein, could complement (ie. rescue) the deletion mutation-caused maternal effect. It therefore appeared that maternally derived fem-1 RNA was required for spermatogenesis, independently of its protein-coding function.

To confirm this, the authors injected in vitro transcribed fem-1 RNA into females homozygous for the fem-1 deletion allele. These worm’s progeny displayed fewer Fog phenotypes than those of uninjected worms. A similar level of rescue was observed when fem-1 RNA without a translation initiation codon was injected, showing that FEM-1 protein was not required.

What was the function of the maternal fem-1 RNA? Johnson and Spence hypothesised that it might be required for normal zygotic fem-1 activity. They therefore assayed this in heterozygotic worms descended either from mothers homozygous for the deletion, or from heterozygotes. Both a genetic test and observation of zygotic fem-1 RNA levels showed that zygotic fem-1 activity in the germline was impaired in the absence of maternal fem-1 RNA.

The authors went on to show that the severity of the Fog phenotypes observed in heterozygotes depended on the history of the wild-type fem-1 allele. Repeatedly backcrossing heterozygotes with homozygotes increased the penetrance of Fog phenotypes in heterozygotes. This showed that although the wild-type allele remains the same genetically, it becomes heritably compromised epigenetically.

To explain these findings, the authors suggest that in the absence of maternal fem-1 RNA, the paternally contributed wild-type allele becomes epigenetically silenced in the zygotic germline. They perspicaciously reasoned that the anti-silencing activity of the maternal RNA may work by inactivating silencing siRNAs, hence licensing zygotic expression. The cluster of recent papers (discussed here) have come to similar conclusions, suggesting the presence of an anti-silencing pathway, possibly mediated by CSR-1 and it’s associated 22G-RNAs.

This epigenetic licensing system effectively marks genes previously expressed in the germline as ‘self’, whilst transcripts without a history of expression are silenced as potentially deleterious. So far the mechanisms of this pathway are yet to be elucidated. As the CSR-1/22G-RNA system targets thousands of genes, one would expect similar phenomena to those observed with fem-1 to be more regularly observed. I’m looking forward to further findings in this field, and potentially analogous systems being discovered in other organisms.

Johnson CL, & Spence AM (2011). Epigenetic licensing of germline gene expression by maternal RNA in C. elegans. Science (New York, N.Y.), 333 (6047), 1311-4 PMID: 21885785

Trans-Extremophile Para-Sex

Cells of Haloferax volcanii showing their cup-like morphology

More than twenty years ago, an extra-ordinary mode of para-sexual genetic exchange was found to occur between cells of the halophilic archaeon Haloferax volcanii, an extremophile isolated from the Dead Sea. This process involves first, cell fusion producing heterodiploid cells. In this state, parental chromosomes can recombine, hence producing novel hybrid daughter cells after cell separation.

Haloferax mediterranei

Naor et al. have now shown that this mechanism of genetic exchange can also occur between cells of H. volcanii, and those of a related species – Haloferax mediterranei. H. mediterranei was originally isolated from a saltern near Alicante in Spain, and shares on average 86.6% sequence identity in protein-coding genes with H. volcanii. Assaying for chromosomal markers, it was found that interspecies cell fusion occurs at a frequency of 4.2 x 10-5, less than one order of magnitude less frequently than between H. volcanii cells (1.0 x 10-4). Of intraspecies fusions, 62% resulted in genetic recombination, whereas only 8% of interspecies fusions did. Although these figures sound quite small, in comparison to modes of genetic exchange between bacterial species, this inter-species genetic interchange occurred  a few orders of magnitude more efficiently.

Analysing a number of hybrid genomes, Naor et al. found that recombinant fragments ranged in size between 310 kb and 530 kb – huge genomic portions, with respect to most known bacterial horizontal genetic transfer mechanisms. Recombination occurs at areas higher sequence identity, such as transfer RNA genes. As these hybrids were isolated by selection for a specific genetic marker, it is quite conceivable, that higher proportions of the genomes can be transferred by this process.

This form of genetic exchange has important implications for archaeal speciation and evolution. High rates of recombination can act as a homogenising force – unlinking alleles faster than genes can diversify. The authors therefore suggest that geographical isolation may be the primary force in archaeal speciation. Further experiments testing the efficiency of this parasexual genetic exchange mechanism between other Haloferax species, and more information on halophilic archaeal ecology will help to clarify these issues. It will also be interesting to examine more hybrid genomes derived from other selection experiments to find out just how extensive interspecies recombination can be and whether there are any directional biases in transfer.

Naor A, Lapierre P, Mevarech M, Papke RT, & Gophna U (2012). Low species barriers in halophilic archaea and the formation of recombinant hybrids. Current biology : CB, 22 (15), 1444-8 PMID: 22748314