Interactions across exons can influence splice site recognition in plant nuclei

Genome Engineering and Agriculture: Opportunities and Challenges

In recent years, plant biotechnology has witnessed unprecedented technological change. Advances in high-throughput sequencing technologies have provided insight into the location and structure of functional elements within plant DNA. At the same time, improvements in genome engineering tools have enabled unprecedented control over genetic material. These technologies, combined with a growing understanding of plant systems biology, will irrevocably alter the way we create new crop varieties. As the first wave of genome-edited products emerge, we are just getting a glimpse of the immense opportunities the technology provides. We are also seeing its challenges and limitations. It is clear that genome editing will play an increased role in crop improvement and will help us to achieve food security in the coming decades; however, certain challenges and limitations must be overcome to realize the technology's full potential.

Revisiting an important component of plant genomes: microsatellites

Microsatellites are some of the most highly variable repetitive DNA tracts in genomes. Few studies focus on whether the characteristic instability of microsatellites is linked to phenotypic effects in plants. We summarise recent data to investigate how microsatellite variations affect gene expression and hence phenotype. We discuss how the basic characteristics of microsatellites may contribute to phenotypic effects. In summary, microsatellites in plants are universal and highly mutable, they coexist and coevolve with transposable elements, and are under selective pressure. The number of motif nucleotides, the type of motif and transposon activity all contribute to the nonrandom generation and decay of microsatellites, and to conservation and distribution biases. Although microsatellites are generated by accident, they mature through responses to environmental change before final decay. This process is mediated by organism adjustment mechanisms, which maintain a balance between birth versus death and growth versus decay in microsatellites. Close relationships also exist between the physical structure, variation and functionality of microsatellites: in most plant species, sequences containing microsatellites are associated with catalytic activity and binding functions, are expressed in the membrane and organelles, and participate in the developmental and metabolic processes. Microsatellites contribute to genome structure and functional plasticity, and may be considered to promote species evolution in plants in response to environmental changes. In conclusion, the generation, loss, functionality and evolution of microsatellites can be related to plant gene expression and functional alterations. The effect of microsatellites on phenotypic variation may be as significant in plants as it is in animals.

Splice site requirements and switches in plants

Intron sequences in nuclear pre-mRNAs are excised with either the major U2 snRNA-dependent spliceosomal pathway or the minor U12 snRNA-dependent spliceosomal pathway that exist in most eukaryotic organisms. While the predominant dinucleotides bordering each of these types of introns and the catalytic mechanism used in their excision are conserved in plants and animals, several features aiding in the recognition of plant introns are distinct from those in animals and yeast. Along with their short length, high AU content and high variation in their 5' and 3' splice sites and branchpoint consensus sequences are the most prominent characteristics of plant introns. Detailed surveys of site-directed mutant introns tested in vivo and chemically induced and naturally mutant introns analyzed in planta emphasize the effects of changing individual nucleotides in these splice site consensus sequences and highlight a number of noncanonical dinucleotides that are functional in plant systems.

Cross-kingdom patterns of alternative splicing and splice recognition

BACKGROUND

Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of splice site recognition inconsistently identifies intron-exon boundaries, and cassette exons (CEs) are often caused by variable recognition of splice junctions by the exon definition (ED) mechanism. We have performed a comprehensive survey of alternative splicing across 42 eukaryotes to gain insight into how spliceosomal introns are recognized.

RESULTS

All eukaryotes we studied exhibit RIs, which appear more frequently than previously thought. CEs are also present in all kingdoms and most of the organisms in our analysis. We observe that the ratio of CEs to RIs varies substantially among kingdoms, while the ratio of competing 3' acceptor and competing 5' donor sites remains nearly constant. In addition, we find the ratio of CEs to RIs in each organism correlates with the length of its introns. In all 14 fungi we examined, as well as in most of the 9 protists, RIs far outnumber CEs. This differs from the trend seen in 13 multicellular animals, where CEs occur much more frequently than RIs. The six plants we analyzed exhibit intermediate proportions of CEs and RIs.

CONCLUSION

Our results suggest that most extant eukaryotes are capable of recognizing splice sites via both ID and ED, although ED is most common in multicellular animals and ID predominates in fungi and most protists.

Coevolutionary networks of splicing cis-regulatory elements

Accurate and efficient splicing of eukaryotic pre-mRNAs requires recognition by trans-acting factors of a complex array of cis-acting RNA elements. Here, we developed a generalized Bayesian network to model the coevolution of splicing cis elements in diverse eukaryotic taxa. Cross-exon but not cross-intron compensatory interactions between the 5' splice site (5'ss) and 3' splice site (3'ss) were observed in human/mouse, indicating that the exon is the primary evolutionary unit in mammals. Studied plants, fungi, and invertebrates exhibited exclusively cross-intron interactions, suggesting that intron definition drives evolution in these organisms. In mammals, 5'ss strength and the strength of several classes of exonic splicing silencers (ESSs) evolved in a correlated way, whereas specific exonic splicing enhancers (ESEs), including motifs associated with hTra2, SRp55, and SRp20, evolved in a compensatory manner relative to the 5'ss and 3'ss. Interactions between specific ESS or ESE motifs were not observed, suggesting that elements bound by different factors are not commonly interchangeable. Thus, the splicing elements defining exons coevolve in a way that preserves overall exon strength, allowing specific elements to substitute for loss or weakening of others.

Alternative splicing of pre-messenger RNAs in plants in the genomic era

Primary transcripts (precursor-mRNAs) with introns can undergo alternative splicing to produce multiple transcripts from a single gene by differential use of splice sites, thereby increasing the transcriptome and proteome complexity within and between cells and tissues. Alternative splicing in plants is largely an unexplored area of gene expression, as this phenomenon used to be considered rare. However, recent genome-wide computational analyses have revealed that alternative splicing in flowering plants is far more prevalent than previously thought. Interestingly, pre-mRNAs of many spliceosomal proteins, especially serine/arginine-rich (SR) proteins, are extensively alternatively spliced. Furthermore, stresses have a dramatic effect on alternative splicing of pre-mRNAs including those that encode many spliceosomal proteins. Although the mechanisms that regulate alternative splicing in plants are largely unknown, several reports strongly suggest a key role for SR proteins in spliceosome assembly and regulated splicing. Recent studies suggest that alternative splicing in plants is an important posttranscriptional regulatory mechanism in modulating gene expression and eventually plant form and function.

Analysis of splice donor and acceptor function in a novel Ac-based gene trap construct

In this study, an Ac-based gene trap construct was engineered to increase gene trapping efficiency by an effective use of triple acceptor sites preceding a reporter gene. The target of the engineering process was a synthetic intron preceding the GUS reporter. Two different gene trap constructs were designed. In one construct, three of the sequence elements serving as signals for recognition of an intron 3' boundary were systematically modified to allow for almost optimal acceptor site recognition, while these sequences remained unchanged in the other construct. To compare recognition of the engineered intron with that of the unmodified intron, tester constructs were transiently transformed into barley (Hordeum vulgare L.) tissue and the accuracy and efficiency of splicing was determined by mRNA mapping and reporter-gene expression frequency analysis. By employing this test system, we could show that systematic engineering of the intron sequence elements results in advanced intron recognition, compared to the unmodified intron, and that all three acceptor sites were activated, but with unequal frequency. The impact of our findings on reporter expression in a gene-trap approach is discussed.

Determinants of plant U12-dependent intron splicing efficiency

Factors affecting splicing of plant U12-dependent introns have been examined by extensive mutational analyses in an in vivo tobacco (Nicotiana tabacum) protoplast system using introns from three different Arabidopsis thaliana genes: CBP20, GSH2, and LD. The results provide evidence that splicing efficiency of plant U12 introns depends on a combination of factors, including UA content, exon bridging interactions between the U12 intron and flanking U2-dependent introns, and exon splicing enhancer sequences (ESEs). Unexpectedly, all three plant U12 introns required an adenosine at the upstream purine position in the branchpoint consensus UCCUURAUY. The exon upstream of the LD U12 intron is a major determinant of its higher level of splicing efficiency and potentially contains two ESE regions. These results suggest that in plants, U12 introns represent a level at which expression of their host genes can be regulated.

Dual functionality of a plant U-rich intronic sequence element

In potato invertase genes, the constitutively included, 9-nucleotide (nt)-long mini-exon requires a strong branchpoint and U-rich polypyrimidine tract for inclusion. The strength of these splicing signals was demonstrated by greatly enhanced splicing of a poorly spliced intron and by their ability to support splicing of an artificial mini-exon, following their introduction. Plant introns also require a second splicing signal, UA-rich intronic elements, for efficient intron splicing. Mutation of the branchpoint caused loss of mini-exon inclusion without loss of splicing enhancement, showing that the same U-rich sequence can function as either a polypyrimidine tract or a UA-rich intronic element. The distinction between the splicing signals depended on intron context (the presence or absence of an upstream, adjacent and functional branchpoint), and on the sequence context of the U-rich elements. Polypyrimidine tracts tolerated C residues while UA-rich intronic elements tolerated As. Thus, in plant introns, U-rich splicing elements can have dual roles as either a general plant U-rich splicing signal or a polypyrimidine tract. Finally, overexpression of two different U-rich binding proteins enhanced intron recognition significantly. These results highlight the importance of co-operation between splicing signals, the importance of other nucleotides within U-rich elements for optimal binding of competing splicing factors and effects on splicing efficiency of U-rich binding proteins.

A splice site mutant of maize activates cryptic splice sites, elicits intron inclusion and exon exclusion, and permits branch point elucidation

DNA sequence analysis of the bt2-7503 mutant allele of the maize brittle-2 gene revealed a point mutation in the 5' terminal sequence of intron 3 changing GT to AT. This lesion completely abolishes use of this splice site, activates two cryptic splice sites, and alters the splicing pattern from extant splice sites. One activated donor site, located nine nt 5' to the normal splice donor site, begins with the dinucleotide GC. While non-consensus, this sequence still permits both trans-esterification reactions of pre-mRNA splicing. A second cryptic site located 23 nt 5' to the normal splice site and beginning with GA, undergoes the first trans-esterification reaction leading to lariat formation, but lacks the ability to participate in the second reaction. Accumulation of this splicing intermediate and use of an innovative reverse transcriptase-polymerase chain reaction technique (J. Vogel, R.H. Wolfgang, T. Borner [1997] Nucleic Acids Res 25: 2030-2031) led to the identification of 3' intron sequences needed for lariat formation. In most splicing reactions, neither cryptic site is recognized. Most mature transcripts include intron 3, while the second most frequent class lacks exon 3. Traditionally, the former class of transcripts is taken as evidence for the intron definition of splicing, while the latter class has given credence to the exon definition of splicing.

The AG dinucleotide terminating introns is important but not always required for pre-mRNA splicing in the maize endosperm

Previous RNA analysis of lesions within the 15 intron-containing Sh2 (shrunken2) gene of maize (Zea mays) revealed that the majority of these mutants affect RNA splicing. Here we decipher further two of these mutants, sh2-i (shrunken2 intermediate phenotype) and sh2-7460. Each harbors a G-to-A transition in the terminal nucleotide of an intron, hence destroying the invariant AG found at the terminus of virtually all nuclear introns. Consequences of the mutations, however, differ dramatically. In sh2-i the mutant site is recognized as an authentic splice site in approximately 10% of the primary transcripts processed in the maize endosperm. The other transcripts exhibited exon skipping and lacked exon 3. A G-to-A transition in the terminus of an intron was also found in the mutant sh2-7460, in this case intron 12. The lesion activates a cryptic acceptor site downstream 22 bp within exon 13. In addition, approximately 50% of sh2-7460 transcripts contain intron 2 and 3 sequences.

Temperature-sensitive splicing in the floral homeotic mutant apetala3-1

The floral homeotic gene APETALA3 (AP3) is required for stamen and petal development in Arabidopsis. The previously described ap3-1 allele is temperature sensitive and carries a missense mutation near a 5' splice site. The missense mutation lies within a domain of the AP3 protein that is thought to be important for protein-protein interactions, which suggests that temperature sensitivity of ap3-1 could reflect an unstable interaction with cofactors. Here, we show instead that the ap3-1 mutation causes a temperature-dependent splicing defect and that temperature sensitivity is not a property of the protein products of ap3-1 but of RNA processing, possibly because of unstable base pairing between the transcript and small nuclear RNAs. The unexpected defect of the ap3-1 mutant offers unique opportunities for genetic and molecular studies of splice site recognition in plants.

An intragenic suppressor of the Arabidopsis floral organ identity mutant apetala3-1 functions by suppressing defects in splicing

The Arabidopsis floral organ identity gene APETALA3 (AP3) specifies the identity of petals and stamens in the flower. In flowers mutant for the temperature-sensitive ap3-1 allele, the petals and stamens are partially converted to sepals and carpels, respectively. ap3-1 contains a single nucleotide change in the AP3 gene that alters both an amino acid in the AP3 protein and the 5' splice consensus site for intron 5. Surprisingly, the Ap3-1 mutant phenotype is not due to the missense mutation but instead is due to defects in splicing; specifically, exon 5 is frequently skipped by the splicing machinery at the restrictive temperature. In a screen for suppressors of ap3-1, we isolated an intragenic suppressor, ap3-11, that functions to suppress the splicing defects of ap3-1. Using a reverse transcriptase-polymerase chain reaction assay, we demonstrate that the percentage of full-length exon 5-containing AP3 RNAs correlates with the phenotype of the flowers in both ap3-1 and ap3-11. Rather surprisingly, the ap3-11 suppressor mutation is located in intron 4. One model explaining the function of ap3-11 is that the ap3-11 suppressor creates a novel branch point sequence that causes exon 5 to be more frequently recognized by the splicing machinery. The identification of such a suppressor strongly suggests that exon-scanning models of intron-exon recognition are operative in plants.

A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5' splice site of the first intron

In cultivated rice two wild-type alleles, Wxa and Wxb, predominate at the waxy locus, which encodes granule-bound starch synthase. The activity of Wxa is 10-fold higher than that of Wxb at the level of both protein and mRNA. Wxb has a +1G to T mutation at the 5' splice site of the first intron. Sequence analysis of Wxb transcripts revealed that splicing occurs at the mutant AG/UU site and at two cryptic sites: the first is A/GUU, one base upstream of the original site and the second is AG/GU found approximately 100 bases upstream of the mutant splice site. We introduced single base mutations to the 5' splice sites of both Wxa and Wxb, fused with the gus reporter gene and introduced them into rice protoplasts. Analysis of GUS activities and transcripts indicated that a G to T mutation in Wxa reduced GUS activity and the level of spliced RNA. Conversely, a T to G mutation of Wxb restored GUS activity and the level of spliced RNA to that of wild-type Wxa. These results demonstrated that the low level expression of Wxb results from a single base mutation at the 5' splice site of the first intron. It is of interest that the Wxb allele of rice carrying the G to T mutation of intron 1 has been conserved in the history of rice cultivation because there is a low amylose content of the seed caused by this mutation.

SPLICE SITE SELECTION IN PLANT PRE-mRNA SPLICING

The purpose of this review is to highlight the unique and common features of splice site selection in plants compared with the better understood yeast and vertebrate systems. A key question in plant splicing is the role of AU sequences and how and at what stage they are involved in spliceosome assembly. Clearly, intronic U- or AU-rich and exonic GC- and AG-rich elements can influence splice site selection and splicing efficiency and are likely to bind proteins. It is becoming clear that splicing of a particular intron depends on a fine balance in the "strength" of the multiple intron signals involved in splice site selection. Individual introns contain varying strengths of signals and what is critical to splicing of one intron may be of less importance to the splicing of another. Thus, small changes to signals may severely disrupt splicing or have little or no effect depending on the overall sequence context of a specific intron/exon organization.

G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection

Splicing of small introns in lower eucaryotes can be distinguished from vertebrate splicing by the inability of such introns to be expanded and by the inability of splice site mutations to cause exon skipping-properties suggesting that the intron rather than the exon is the unit of recognition. Vertebrates do contain small introns. To see if they possess properties similar to small introns in lower eucaryotes, we studied the small second intron from the human alpha-globin gene. Mutation of the 5' splice site of this intron resulted in in vivo intron inclusion, not exon skipping, suggesting the presence of intron bridging interactions. The intron had an unusual base composition reflective of a sequence bias present in a collection of small human introns in which multiple G triplets stud the interior of the introns. Each G triplet represented a minimal sequence element additively contributing to maximal splicing efficiency and spliceosome assembly. More importantly, G triplets proximal to a duplicated splice site caused preferential utilization of the 5' splice site upstream of the triplets or the 3' splice site downstream of the triplets; i.e., sequences containing G triplets were preferentially used as introns when a choice was possible. Thus, G triplets internal to a small intron have the ability to affect splice site decisions at both ends of the intron. Each G triplet additively contributed to splice site selectivity. We suggest that G triplets are a common component of human 5' splice sites and aid in the definition of exon-intron borders as well as overall splicing efficiency. In addition, our data suggest that such intronic elements may be characteristic of small introns and represent an intronic equivalent to the exon enhancers that facilitate recognition of both ends of an exon during exon definition.