Neurospora msh 4 ortholog confirmed by split-marker deletion

Although most eukaryotes have both MSH4 and MSH5 orthologs, Neurospora was initially thought to lack msh-4. We have deleted the most likely msh-4 candidate and observed a delay in the sexual cycle, disruption to meiosis and a reduction in fertility. Deletion is dominant, showing msh-4 is subject to MSUD. We conclude that Neurospora has a MSH4 ortholog and that it may have remained undetected because of an unusually high number of introns. Creative Commons License This work is licensed under a Creative Commons Attribution-Share Alike 4.0 License. This regular paper is available in Fungal Genetics Reports: http://newprairiepress.org/fgr/vol53/iss1/2


Neurospora msh4 ortholog confirmed by split-marker deletion
Sue Conway, Fred Bowring, Jane Yeadon and David Catcheside.School of Biological Sciences, Flinders University, PO Box 2100, Adelaide, South Australia 5001 Fungal Genetics Newsletter 53:5-8 Although most eukaryotes have both MSH4 and MSH5 orthologs, Neurospora was initially thought to lack msh4.We have deleted the most likely msh4 candidate and observed a delay in the sexual cycle, disruption to meiosis and a reduction in fertility.Deletion is dominant, showing msh4 is subject to MSUD.We conclude that Neurospora has an MSH4 ortholog and that it may have remained undetected because of an unusually high number of introns.
MSH4, a member of the MutS protein family, is conserved in higher organisms and has a role in crossover regulation.Disruption of MSH4 reduces the frequency of crossing over in many organisms (Ross-Macdonald and Roeder, 1994;Zalevsky et al., 1999) and increases the incidence of chromosomal non-disjunction, identical phenotypes to that of MSH5 mutants (Hollingsworth et al., 1995;Hunter et al., 1997).MSH4 and MSH5 function as a heterodimer, and removal of the ATPase domain from either leads to loss of function (Alani, 1997;Haber and Walker, 1991;Pochart et al., 1997).All MSH4 orthologs contain MutS DNA-binding and ATPase domains.MSH4 also seems to have a role in the formation or elongation of the synaptonemal complex, a proteinaceous structure that holds homologous chromosomes in close proximity prior to the reductional division of meiosis.Chromosome synapsis is delayed and incomplete in Saccharomyces cerevisiae MSH4 mutants (Novak et al., 2001), and MSH4 localises at synapsis initiation sites in both yeast and mammalian meiotic cells (Novak et al., 2001;Neyton et al., 2004).
Gene prediction algorithms used in the Neurospora genome project failed to identify an MSH4 ortholog.A subsequent bioinformatic analysis used tBlastn to identify a region with homology to MSH4 sequences of S. cerevisiae, Mouse and Human (Borkovich et al., 2004).Alignment of the predicted protein sequence with human and S. cerevisiae MSH4 protein sequences using ClustalW showed that Neurospora MSH4 shares conserved regions with the other two amino acid sequences (figure 1).
We concluded that the msh4 gene is about 3 kb in length (figure 2), and is located on LG1R, between met-6 and aap-2, on supercontig 7.2, nucleotide positions 1061633-1064675.
A 3.2 kb sequence including the potential msh4 gene was analysed using GenScan (Burge and Karlin, 1997) to identify possible coding sequence and to suggest possible amino acid sequences by removing introns predicted by identification of eukaryotic splice sites (figure 2).Using either human or Arabidopsis parameters gave very similar results.
Analysis of the predicted 871 amino acid sequence using Motifs (GCG: Wisconsin Package ) identified a potential gene with TM an ATP/GTP binding site and a DNA MMR motif.Use of a CD search, which identifies conserved domains within a protein sequence by comparing the sequence with other known protein sequences (Marchler-Bauer et al. 2005), identified a MutS homolog with a DNA binding mismatch repair domain (MUTSd) and an ATPase domain (MUTSac; figure 3).
Thus, Msh4 appears to possess DNA-binding and ATPase domains as expected, and it seems likely that there are six introns (figure 2) within the msh4 nucleotide sequence.Since Neurospora genes have, on average, 1.7 introns (Borkovich et al., 2004), the unusually large number in this msh4 candidate might explain why it was missed by the gene prediction algorithms.
Published by New Prairie Press, 2017  Using split-marker deletion (Catlett et al., 2003), we replaced the predicted msh4 sequence with the hygromycin resistance gene (hph) in a mating pair of Neurospora strains, and analysed the effect through comparison of crosses that are isogenic except for the msh4 deletion.Gross perithecial morphology seems to be unaffected by the deletion, although ejection of the first spores is delayed by ~2 days in mutant crosses.There is a 5-fold reduction in viable spores recovered from Dmsh4 homoand hetero-zygotes (mutant average = 2 x 10 spores per cross, untransformed control = 1 x 10 spores per cross), and mutant 56 crosses yield many more white spores.Sporogenesis in homozygous and heterozygous Dmsh4 crosses is delayed and rosettes from the Dmsh4 mutants contain more bubble asci (Perkins and Barry, 1977) and fewer normal size asci than the control.Asci containing less than eight spores or at least one misshapen spore are common in Dmsh4 crosses, regardless of whether the mutant is the male or female parent, but rarely observed in the control (figure 4).A cursory analysis of chromosomal behaviour during meiosis suggests that an absence of msh4 causes some abnormality, although at this stage we have not found evidence of non-disjunction during meiosis I. Published by New Prairie Press, 2017 In conclusion, deletion of the putative Neurospora msh4 gene interferes with sporogenesis and possibly meiosis.The deletion appears dominant, suggesting that msh4 is normally expressed during meiosis and subject to meiotic silencing of unpaired DNA (Shiu and Metzenberg, 2002).The msh4 candidate we deleted contains the MutS and ATPase domains common to all MSH4 orthologs and shares considerable predicted amino acid identity with both yeast and mammalian MSH4 proteins.Since we have now demonstrated a role for this gene in the sexual phase it is likely that it is indeed the Neurospora ortholog of MSH4.

Figure 1 .
Figure 1.Alignment of the human (Hs) and Yeast (Sc) MSH4 proteins with the Neurospora (Nc) predicted 871 amino acid sequence.Dark shading represents identical and lighter shading similar residues.

Figure 2 .
Figure 2. GenScan graphical representation of predicted coding sequences within the putative msh4 nucleotide sequence.The gaps between blocks represent predicted introns.