RESEARCH ARTICLES CURRENT SCIENCE, VOL. 114, NO. 8, 25 APRIL 2018 1677 *For correspondence. (e-mail: abhishek.abhishekkumar@gmail.com) Spliceosomal proteins encoded by fungal genomes Sandeep J. Sarde 1 , Frank Kempken 1 and Abhishek Kumar 1,2, * 1 Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40 24098 Kiel, Germany 2 Present address: Molecular Genetic Epidemiology (C050), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580 69120 Heidelberg, Germany A large number of spliceosomal proteins are required for proper RNA splicing. While spliceosomal proteins from several model organisms have been analysed, only limited studies are available for fungal species. Hence, we have performed a comparative genomic analysis using eight fungal species belonging to three taxa (Ascomycetes, Basidiomycetes and Glomeromy- cota). We identified variable number of spliceosomal proteins in fungal species. From the small nuclear ribonucleoproteins (snRNPs), all the snRNPs were identified. In non-snRNPs, only some sub-groups were found extensively conserved in all fungal species, in- cluding PRP19 complex proteins, catalytic step II and late-acting proteins. In heterogeneous nuclear ribonu- cleoproteins (hnRNPs), variable number of proteins was identified. The number of spliceosomal proteins identified in filamentous fungi was higher than that in yeast. The collection of these spliceosomal proteins pro- vides further insight into pre-mRNA splicing in fungi. Keywords: Fungal genomes, pre-mRNA, snRNPs, spliceosomal proteins. IN eukaryotes, genes are interrupted with non-coding sequences (introns), which are transcribed into pre-mRNA in the nucleus. The pre-mRNA is then processed and this results in the splicing out of introns to give yield a mature mRNA. This process, called splicing 1 , serves as one of the hallmarks of eukaryotic genetics and is a crucial mechanism for eukaryotic messenger RNAs before they get translated into functional proteins 2 . This process is catalysed by the spliceosome, a multi-component macro- molecular machine 3–5 . The spliceosome is a multi-mega- dalton ribonucleoprotein (RNP) complex comprising of pre-mRNA template, small nuclear ribonucleoproteins (snRNPs) and different non-snRNPs 1,6 . Further back- ground of different groups of spliceosomal proteins is provided below and in Supplementary Section 1. The snRNPs are core constituents of the spliceosomal complex which regulate pre-mRNA splicing and are com- prised of a unique small nuclear ribonucleic acid (snRNA), a common set of Sm proteins (Sm-B⁄SmB’, SmD1, SmD2, SmD3, SmE, SmF and SmG) and diverse number of snRNP specific proteins 7 . The U2 dependent spliceo- some is assembled from the U1, U2, U5, U4/U6 snRNPs, and an abundant number of non-snRNP proteins. In con- trast, the U12-dependent spliceosome is assembled from U11, U12, U5 and U4atac/U6atac snRNPs 6 . These differ- ent snRNPs are classified into Sm/LSm core proteins, U1, U2, U5, U4/U6 specific proteins and tri-snRNP specific proteins 8 . Sm/LSm proteins are present ubiquitously in eukary- otes. They interact with RNAs to make complexes, thus taking part in nearly every cellular process. Due to struc- tural similarity with Sm proteins, they are called ‘Like Sm’ or ‘LSm’ proteins 9 . Sm proteins are a set of small polypeptides that play a critical role in gathering the U1, U2, U5 and U4/U6 snRNPs for pre-mRNA splicing 10 . Sm proteins are differentiated into seven sub-classes based on human Sm proteins, which are known as SmB, SmD1, SmD2, SmD3, SmE, SmF and SmG. There are a total of nine LSm proteins (LSm1 to LSm9) existing in S. cere- visiae, of which, LSm2 to LSm7 appear to be very similar to SmD1 to SmG respectively 11 . In contrast, LSm1 and LSm8 seem to be more similar to the SmB sub-family 11,12 . The U1 snRNP is a vital member of the spliceosomal snRNPs. Human U1 snRNP consists of several specific and unique snRNPs including 164-nucleotide U1 small nuclear RNA (U1SnRNA) 13 . In metazoans, splicing mechanism is initiated by U1snRNA (part of U1 snRNP), by recognizing 5-splice-site (5-ss) and forming the E- complex. Subsequently, this base pairing of U1RNA is stabilized by U1 snRNP specific proteins named U1-70K and U1-C 7 . U2 snRNP firmly associates with the branching site 14 after the U1 snRNP, forming pre-spliceosomal complex A or pre-spliceosome complex. U2 snRNP plays a main part in splicing after the dissociation of U1 and U4 snRNP from pre-mRNA. A wide ranging base pairing system and conformational changes are shaped between U6 and U2 snRNP, which juxtaposes the branch site (BS) and 5 -ss for the initial step of splicing 6 . Many eukaryotic genes are expressed as precursor mRNAs by RNA polymerase II, which are further