The fungal mitochondrial Nad5 pan-genic intron landscape

References

• Abboud TG, Zubaer A, Wai A, Hausner G. 2018. The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi. Can J Microbiol. 64(5):339–348.
   PubMed Web of Science ®Google Scholar
• Baidyaroy D, Hausner G, Hafez M, Michel F, Fulbright DW, Bertrand H. 2011. A 971-bp insertion in the rns gene is associated with mitochondrial hypovirulence in a strain of Cryphonectria parasitica isolated from nature. Fungal Genet Biol. 48(8):775–783.
   PubMed Web of Science ®Google Scholar
• Belfort M. 2003. Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase. Genes Dev. 17(23):2860–2863. Cold Spring Harbor Laboratory Press.
   PubMed Web of Science ®Google Scholar
• Belfort M, Derbyshire V, Parker MM, Cousineau B, Lambowitz AM. 2002. Mobile Introns: Pathways and proteins. In: Craig NL, Craigie R, Gellert M, Lambowitz AM, ediors. Mobile DNA II. Washington (DC): ASM Press; pp. 761–783.
   Google Scholar
• Cummings DJ, McNally KL, Domenico JM, Matsuura ET. 1990. The complete DNA sequence of the mitochondrial genome of Podospora anserina. Curr Genet. 17(5):375–402.
   PubMed Web of Science ®Google Scholar
• Deng Y, Hsiang T, Li S, Lin L, Wang Q, Chen Q, Xie B, Ming R. 2018. Comparison of the mitochondrial genome sequences of six Annulohypoxylon stygium isolates suggests short fragment insertions as a potential factor leading to larger genomic size. Front Microbiol. 9:2079.
   PubMed Web of Science ®Google Scholar
• Edgell DR, Chalamcharla VR, Belfort M. 2011. Learning to live together: mutualism between self-splicing introns and their hosts. BMC Biol. 9(1):22.
   PubMedGoogle Scholar
• Emblem Å, Okkenhaug S, Weiss ES, Denver DR, Karlsen BO, Moum T, Johansen SD. 2014. Sea anemones possess dynamic mitogenome structures. Mol Phylogenet Evol. 75:184–193.
   PubMed Web of Science ®Google Scholar
• Enyeart PJ, Mohr G, Ellington AD, Lambowitz AM. 2014. Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis. Mob DNA. 5(1):2.
   PubMedGoogle Scholar
• Fedorova O, Jagdmann GE, Jr, Adams RL, Yuan L, Van Zandt MC, Pyle AM. 2018. Small molecules that target group II introns are potent antifungal agents. Nat Chem Biol. 14(12):1073–1078.
   PubMed Web of Science ®Google Scholar
• Férandon C, Moukha S, Callac P, Benedetto J-P, Castroviejo M, Barroso G. 2010. The Agaricus bisporus cox1 gene: the longest mitochondrial gene and the largest reservoir of mitochondrial group I introns. PLoS One. 5(11):e14048.
   PubMed Web of Science ®Google Scholar
• Freel KC, Friedrich A, Schacherer J. 2015. Mitochondrial genome evolution in yeasts: an all-encompassing view. FEMS Yeast Res. 15:1–9.
   Web of Science ®Google Scholar
• Goddard MR, Burt A. 1999. Recurrent invasion and extinction of a selfish gene. Proc Natl Acad Sci USA. 96(24):13880–13885.
   PubMed Web of Science ®Google Scholar
• Gogarten JP, Hilario E. 2006. Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements. BMC Evol Biol. 6:94.
   PubMed Web of Science ®Google Scholar
• Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, Riley R, Salamov A, Zhao X, Korzeniewski F, et al. 2014. MycoCosm portal: gearing up for 1000 fungal genomes. Nucl Acids Res. 42(D1):D699–704.
   PubMed Web of Science ®Google Scholar
• Guha KT, Hausner G. 2016. Using group II introns for attenuating the in vitro and in vivo expression of a homing endonuclease. PLoS One. 11(2):e0150097.
   PubMed Web of Science ®Google Scholar
• Guha TK, Wai A, Hausner G. 2017. Programmable genome editing tools and their regulation for efficient genome engineering. Comput Struct Biotechnol J. 15:146–160.
   PubMed Web of Science ®Google Scholar
• Guha TK, Wai A, Mullineux S-T, Hausner G. 2018. The intron landscape of the mtDNA cytb gene among the Ascomycota: introns and intron-encoded open reading frames. Mitochondrial DNA Part A. 29(7):1015–1024.
   PubMed Web of Science ®Google Scholar
• Haack DB, Yan X, Zhang C, Hingey J, Lyumkis D, Baker TS, Toor N. 2019. Cryo-EM Structures of a group II intron reverse splicing into DNA. Cell. 178(3):612–623. e12.
   PubMed Web of Science ®Google Scholar
• Hafez M, Guha TK, Shen C, Sethuraman J, Hausner G. 2004. PCR-based bioprospecting for homing endonucleases in fungal mitochondrial rRNA genes. Methods Mol Biol. 1123:37–53.
   Google Scholar
• Hafez M, Hausner G. 2012. Homing endonucleases: DNA scissors on a mission. Genome. 55(8):553–569.
   PubMed Web of Science ®Google Scholar
• Hafez M, Hausner G. 2015. Convergent evolution of twintron-like configurations: one is never enough. RNA Biol. 12(12):1275–1288.
   PubMed Web of Science ®Google Scholar
• Hafez M, Majer A, Sethuraman J, Rudski SM, Michel F, Hausner G. 2013. The mtDNA rns gene landscape in the Ophiostomatales and other fungal taxa: Twintrons, introns, and intron-encoded proteins. Fungal Genet. Biol. 53:71–83.
   PubMed Web of Science ®Google Scholar
• Haugen P, Bhattacharya D. 2004. The spread of LAGLIDADG homing endonuclease genes in rDNA. Nucleic Acids Res. 32(6):2049–2057.
   PubMed Web of Science ®Google Scholar
• Hausner G. 2012. Introns, mobile elements, and plasmids. In: Bullerwell CE, editor. Organelle genetics – evolution of organelle genomes and gene expression. New York (NY): Springer-Verlag; p. 329–358.
   Google Scholar
• James TY, Pelin A, Bonen L, Ahrendt S, Sain D, Corradi N, Stajich JE. 2013. Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia. Curr Biol. 23(16):1548–1553.
   PubMed Web of Science ®Google Scholar
• Johansen S, Haugen P. 2001. A new nomenclature of group I introns in ribosomal DNA. RNA. 7(7):935–936.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. 2013. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
   PubMed Web of Science ®Google Scholar
• Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19(9):1639–1645.
   PubMed Web of Science ®Google Scholar
• Lambowitz AM, Belfort M. 2015. Mobile bacterial group II introns at the crux of eukaryotic evolution. Microbiol Spectr. 3(1). MDNA3-0050-2014.
   PubMed Web of Science ®Google Scholar
• Lang BF, Laforest M-J, Burger G. 2007. Mitochondrial introns: a critical view. Trends Genet. 23(3):119–125.
   PubMed Web of Science ®Google Scholar
• Larsson A. 2014. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics. 30(22):3276–3278.
   PubMed Web of Science ®Google Scholar
• Lehnert V, Jaeger L, Michel F, Westhof E. 1996. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem Biol. 3(12):993–1009.
   PubMedGoogle Scholar
• Li CF, Costa M, Bassi G, Lai YK, Michel F. 2011. Recurrent insertion of 5'-terminal nucleotides and loss of the branchpoint motif in lineages of group II introns inserted in mitochondrial preribosomal RNAs. RNA. 17(7):1321–1335.
   PubMed Web of Science ®Google Scholar
• Long M, Rosenberg C, Gilbert W. 1995. Intron phase correlations and the evolution of the intron/exon structure of genes. Proc Natl Acad Sci USA. 92(26):12495–12499.
   PubMed Web of Science ®Google Scholar
• Marcia M, Somarowthu S, Pyle AM. 2013. Now on display: a gallery of group II intron structures at different stages of catalysis. Mob DNA. 4(1):14.
   PubMedGoogle Scholar
• Martin W, Koonin EV. 2006. Introns and the origin of nucleus-cytosol compartmentalization. Nature. 440(7080):41–45.
   PubMed Web of Science ®Google Scholar
• McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR. 2018. Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases. Nucleic Acids Res. 46(22):11990–12007.
   PubMed Web of Science ®Google Scholar
• Michel F, Costa M, Westhof E. 2009. The ribozyme core of group II introns: a structure in want of partners. Trends Biochem Sci. 34(4):189–199.
   PubMed Web of Science ®Google Scholar
• Michel F, Ferat JL. 1995. Structure and activities of group II introns. Annu Rev Biochem. 64(1):435–461.
   PubMedGoogle Scholar
• Michel F, Westhof E. 1990. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol. 216(3):585–610.
   PubMed Web of Science ®Google Scholar
• Mullineux ST, Costa M, Bassi GS, Michel F, Hausner G. 2010. A group II intron encodes a functional LAGLIDADG homing endonuclease and self-splices under moderate temperature and ionic conditions. RNA. 16(9):1818–1831.
   PubMed Web of Science ®Google Scholar
• Parmeciano Di Noto G, Molina MC, Quiroga C. 2019. Insights Into non-coding RNAs as novel antimicrobial drugs. Front Genet. 10:57.
   PubMed Web of Science ®Google Scholar
• Pfeifer A, Martin B, Kämper J, Basse CW. 2012. The mitochondrial LSU rRNA group II intron of Ustilago maydis encodes an active homing endonuclease likely involved in intron mobility. PLoS One. 7(11):e49551.
   PubMed Web of Science ®Google Scholar
• Pogoda CS, Keepers KG, Nadiadi AY, Bailey DW, Lendemer JC, Tripp EA, Kane NC. 2019. Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria. Ecol Evol. 9(7):4245–4263.
   PubMed Web of Science ®Google Scholar
• Scalley-Kim M, McConnell-Smith A, Stoddard BL. 2007. Coevolution of a homing endonuclease and its host target sequence. J Mol Biol. 372(5):1305–1319.
   PubMed Web of Science ®Google Scholar
• Sethuraman J, Rudski SM, Wosnitza K, Hafez M, Guppy B, Hausner G. 2013. Evolutionary dynamics of introns and their open reading frames in the U7 region of themitochondrial rnl gene in species of Ceratocystis. Fungal Biol. 117(11–12):791–806.
   PubMed Web of Science ®Google Scholar
• Smathers CM, Robart AR. 2009. The mechanism of splicing as told by group II introns: ancestors of the spliceosome. Biochim Biophys Acta Gene Regul Mech. doi:10.1016/j.bbagrm.2019.06.001
   Google Scholar
• Stoddard BL. 2006. Homing endonucleases structure and function. Quart Rev Biophys. 38(01):49–95.
   Google Scholar
• Stoddard BL. 2014. Homing endonucleases from mobile group I introns: discovery to genome engineering. Mob DNA. 5(1):7.
   PubMedGoogle Scholar
• Sullenger BA, Gilboa E. 2002. Emerging clinical applications of RNA. Nature. 418(6894):252–258.
   PubMed Web of Science ®Google Scholar
• Sverdlov AV, Babenko VN, Rogozin IB, Koonin EV. 2004. Preferential loss and gain of introns in 3' portions of genes suggests a reverse-transcription mechanism of intron insertion. Gene. 338(1):85–91.
   PubMed Web of Science ®Google Scholar
• Takeuchi R, Lambert AR, Mak AN, Jacoby K, Dickson RJ, Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL. 2011. Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proc Natl Acad Sci USA. 108(32):13077–13082.
   PubMed Web of Science ®Google Scholar
• Toor N, Hausner G, Zimmerly S. 2001. Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA. 7(8):1142–1152.
   PubMed Web of Science ®Google Scholar
• Toor N, Zimmerly S. 2002. Identification of a family of group II introns encoding LAGLIDADG ORFs typical of group I introns. RNA. 8(11):1373–1377.
   PubMed Web of Science ®Google Scholar
• Wai A, Shen C, Carta A, Dansen A, Crous PW, Hausner G. 2019. Intron-encoded ribosomal proteins and N-acetyltransferases within the mitochondrial genomes of fungi: here today, gone tomorrow? Mitochondrial DNA Part A. 30(3):573–584.
   PubMed Web of Science ®Google Scholar
• Yin L-F, Hu M-J, Wang F, Kuang H, Zhang Y, Schnabel G, Li G-Q, Luo C-X. 2012. Frequent gain and loss of introns in fungal cytochrome b genes. PLoS One. 7(11):e49096.
   PubMed Web of Science ®Google Scholar
• Yoon H, You YH, Woo JR, Park YJ, Kong WS, Lee BM, Kim JG. 2012. The mitochondrial genome of the white-rot fungus Flammulina velutipes. J Gen Appl Microbiol. 58(4):331–337.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Bell A, Perlman PS, Leibowitz MJ. 2000. Pentamidine inhibits mitochondrialintron splicing and translation in Saccharomyces cerevisiae. RNA. 6(7):937–951.
   PubMed Web of Science ®Google Scholar
• Zhao C, Pyle AM. 2017. The group II intron maturase: a reverse transcriptase and splicing factor go hand in hand. Curr Opin Struct Biol. 47:30–39.
   PubMed Web of Science ®Google Scholar
• Zimmerly S, Semper C. 2015. Evolution of group II introns. Mob Dna. 6:7.
   PubMed Web of Science ®Google Scholar
• Zubaer A, Wai A, Hausner G. 2018. The mitochondrial genome of Endoconidiophora resinifera is intron rich. Sci Rep. 8(1):17591.
   PubMedGoogle Scholar
• Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31(13):3406–3415.
   PubMed Web of Science ®Google Scholar