Distribution, organization an evolutionary history of La and LARPs in eukaryotes

References

• Maraia RJ, Mattijssen S, Cruz-Gallardo I, et al. The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives. Wiley Interdiscip Rev RNA. 2017;8(6):e1430.
   PubMed Web of Science ®Google Scholar
• Bousquet-Antonelli C, Deragon J. A comprehensive analysis of the La-motif protein superfamily. RNA. 2009;15(5):750–764.
   PubMed Web of Science ®Google Scholar
• Bayfield MA, Yang R, Maraia RJ. Conserved and divergent features of the structure and function of La and La-related proteins (LARPs). Biochim Biophys Acta. 2010;1799(5–6):365–378.
   PubMed Web of Science ®Google Scholar
• Wolin SL, Cedervall T. The La protein. Annu Rev Biochem. 2002;71(1):375–403.
   PubMedGoogle Scholar
• Chakshusmathi G. A La protein requirement for efficient pre-tRNA folding. EMBO J. 2003;22(24):6562–6572.
   PubMed Web of Science ®Google Scholar
• Krueger BJ, Jeronimo C, Roy BB, et al. LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. Nucleic Acids Res. 2008;36(7):2219–2229. DOI:10.1093/nar/gkn061.
   PubMed Web of Science ®Google Scholar
• Markert A, Grimm M, Martinez J, et al. The La-related protein LARP7 is a component of the 7SK ribonucleoprotein and affects transcription of cellular and viral polymerase II genes. EMBO Rep. 2008;9(6):569–575. DOI:10.1038/embor.2008.72.
   PubMed Web of Science ®Google Scholar
• Aigner S, Postberg J, Lipps HJ, et al. The Euplotes La motif protein p43 has properties of a telomerase-specific subunit. Biochemistry. 2003;42(19):5736–5747.
   PubMed Web of Science ®Google Scholar
• Witkin KL. Holoenzyme proteins required for the physiological assembly and activity of telomerase. Genes Dev. 2004;18(10):1107–1118.
   PubMed Web of Science ®Google Scholar
• Páez-Moscoso DJ, Pan L, Sigauke RF, et al. Pof8 is a La-related protein and a constitutive component of telomerase in fission yeast. Nat Commun. 2018;9(1):587.
   PubMedGoogle Scholar
• Mennie AK, Moser BA, Nakamura TM. LARP7-like protein Pof8 regulates telomerase assembly and poly(A)+TERRA expression in fission yeast. Nat Commun. 2018;9(1):586.
   PubMedGoogle Scholar
• Collopy LC, Ware TL, Goncalves T, et al. LARP7 family proteins have conserved function in telomerase assembly. Nat Commun. 2018;9(1):557. DOI:10.1038/s41467-017-02296-4.
   PubMedGoogle Scholar
• Deragon J-M, Bousquet-Antonelli C. The role of LARP1 in translation and beyond. Wiley Interdiscip Rev RNA. 2015;6(4):399–417.
   PubMed Web of Science ®Google Scholar
• Merret R, Descombin J, Juan YT, et al. XRN4 and LARP1 are required for a heat-triggered mRNA decay pathway involved in plant acclimation and survival during thermal stress. Cell Rep. 2013;5(5):1279–1293. DOI:10.1016/j.celrep.2013.11.019.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Stefanovic B. LARP6 Meets Collagen mRNA: Specific Regulation of Type I Collagen Expression. Int J Mol Sci. 2016;17:419.
   PubMed Web of Science ®Google Scholar
• Intine RV, Tenenbaum SA, Sakulich AL, et al. Differential phosphorylation and subcellular localization of La RNPs associated with precursor tRNAs and translation-related mRNAs. Mol Cell. 2003;12(5):1301–1307.
   PubMed Web of Science ®Google Scholar
• Mattijssen S, Arimbasseri AG, Iben JR, et al. LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection. Elife. 2017;6. DOI:10.7554/eLife.28889.
   PubMed Web of Science ®Google Scholar
• Küspert M, Murakawa Y, Schäffler K, et al. LARP4B is an AU-rich sequence associated factor that promotes mRNA accumulation and translation. RNA. 2015;21(7):1294–1305. DOI:10.1261/rna.051441.115.
   PubMed Web of Science ®Google Scholar
• Fonseca BD, Lahr RM, Damgaard CK, et al. LARP1 on TOP of ribosome production. Wiley Interdiscip Rev RNA. 2018;9(5):e1480.
   PubMed Web of Science ®Google Scholar
• Stavraka C, Blagden S. The La-Related Proteins, a Family with Connections to Cancer. Biomolecules. 2015;5(4):2701–2722.
   PubMed Web of Science ®Google Scholar
• Fonseca BD, Zakaria C, Jia JJ, et al. La-related Protein 1 (LARP1) Represses Terminal Oligopyrimidine (TOP) mRNA Translation Downstream of mTOR Complex 1 (mTORC1). J Biol Chem. 2015;290:15996–16020.
   PubMed Web of Science ®Google Scholar
• Merret R, Martino L, Bousquet-Antonelli C, et al. The association of a La module with the PABP-interacting motif PAM2 is a recurrent evolutionary process that led to the neofunctionalization of La-related proteins. RNA. 2013;19(1):36–50. DOI:10.1261/rna.035469.112.
   PubMed Web of Science ®Google Scholar
• Yang R, Gaidamakov SA, Xie J, et al. La-related protein 4 binds poly(A), interacts with the poly(A)-binding protein MLLE domain via a variant PAM2w motif, and can promote mRNA stability. Mol Cell Biol. 2011;31:542–556.
   PubMed Web of Science ®Google Scholar
• Cruz-Gallardo I, Martino L, Kelly G, et al. LARP4A recognizes polyA RNA via a novel binding mechanism mediated by disordered regions and involving the PAM2w motif, revealing interplay between PABP, LARP4A and mRNA. Nucleic Acids Res. 2019;47(8):4272–4291. DOI:10.1093/nar/gkz144.
   PubMed Web of Science ®Google Scholar
• Wendte JM, Haag JR, Singh J, et al. Functional Dissection of the Pol V Largest Subunit CTD in RNA-Directed DNA Methylation. Cell Rep. 2017;19(13):2796–2808.
   PubMed Web of Science ®Google Scholar
• Lahmy S, Guilleminot J, Cheng CM, et al. DOMINO1, a member of a small plant-specific gene family, encodes a protein essential for nuclear and nucleolar functions. Plant J. 2004;39(6):809–820. DOI:10.1111/tpj.2004.39.issue-6.
   PubMed Web of Science ®Google Scholar
• Bellaoui M, Keddie JS, Gruissem W. DCL is a plant-specific protein required for plastid ribosomal RNA processing and embryo development. Plant Mol Biol. 2003;53:531–543.
   PubMed Web of Science ®Google Scholar
• Wang Y, Ma H. Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits. New Phytol. 2015;207(4):1198–1212.
   PubMed Web of Science ®Google Scholar
• Fleurdedine S, Deragon J, Devic M, et al. A bona fide La protein is required for embryogenesis in Arabidopsis thaliana. Nucleic Acids Res. 2007;35(10):3306–3321. DOI:10.1093/nar/gkm200.
   PubMed Web of Science ®Google Scholar
• Kershaw CJ, Costello JL, Castelli LM, et al. The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response. PLoS Genet. 2015;11:e1004903.
   PubMed Web of Science ®Google Scholar
• Röther S, Burkert C, Brünger KM, et al. Nucleocytoplasmic shuttling of the La motif-containing protein Sro9 might link its nuclear and cytoplasmic functions. RNA. 2010;16(7):1393–1401.
   PubMed Web of Science ®Google Scholar
• Schenk L, Meinel DM, Strässer K, et al. La-motif-dependent mRNA association with Slf1 promotes copper detoxification in yeast. RNA. 2012;18(3):449–461.
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–1797.
   PubMed Web of Science ®Google Scholar
• Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25(15):1972–1973.
   PubMed Web of Science ®Google Scholar
• Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696–704.
   PubMed Web of Science ®Google Scholar
• Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol. 2008;25(7):1307–1320.
   PubMed Web of Science ®Google Scholar
• Anisimova M, Gascuel O. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol. 2006;55(4):539–552.
   PubMed Web of Science ®Google Scholar
• Kelley LA, Sternberg MJ. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc. 2009;4(3):363–371.
   PubMed Web of Science ®Google Scholar
• Riwika Basu CDE, Cheng R, Feigon J. Structure of S. pombe telomerase protein Pof8 C-terminal domain is an xRRM conserved among LARP7 proteins. bioRxiv. 2019;739532. DOI:10.1101/739532.
   Google Scholar