Members of a Large Retroposon Family Are Determinants of Post-Transcriptional Gene Expression in Leishmania

Trypanosomatids are unicellular protists that include the human pathogens Leishmania spp. (leishmaniasis), Trypanosoma brucei (sleeping sickness), and Trypanosoma cruzi (Chagas disease). Analysis of their recently completed genomes confirmed the presence of non–long-terminal repeat retrotransposons, also called retroposons. Using the 79-bp signature sequence common to all trypanosomatid retroposons as bait, we identified in the Leishmania major genome two new large families of small elements—LmSIDER1 (785 copies) and LmSIDER2 (1,073 copies)—that fulfill all the characteristics of extinct trypanosomatid retroposons. LmSIDERs are ∼70 times more abundant in L. major compared to T. brucei and are found almost exclusively within the 3′-untranslated regions (3′UTRs) of L. major mRNAs. We provide experimental evidence that LmSIDER2 act as mRNA instability elements and that LmSIDER2-containing mRNAs are generally expressed at lower levels compared to the non-LmSIDER2 mRNAs. The considerable expansion of LmSIDERs within 3′UTRs in an organism lacking transcriptional control and their role in regulating mRNA stability indicate that Leishmania have probably recycled these short retroposons to globally modulate the expression of a number of genes. To our knowledge, this is the first example in eukaryotes of the domestication and expansion of a family of mobile elements that have evolved to fulfill a critical cellular function.

[1]  D. Haussler,et al.  A distal enhancer and an ultraconserved exon are derived from a novel retroposon , 2006, Nature.

[2]  M. Miya,et al.  V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. , 2002, Genome research.

[3]  J. S. Cordingley,et al.  Complete nucleotide sequence of an unusual mobile element from trypanosoma brucei , 1984, Cell.

[4]  A. Smit,et al.  Functional noncoding sequences derived from SINEs in the mammalian genome. , 2006, Genome research.

[5]  J. Deragon,et al.  Similar Target Site Selection Occurs in Integration of Plant and Mammalian Retroposons , 1998, Journal of Molecular Evolution.

[6]  N. Okada,et al.  LINEs Mobilize SINEs in the Eel through a Shared 3′ Sequence , 2002, Cell.

[7]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[8]  P. Tebabi,et al.  Trypanosoma brucei repeated element with unusual structural and transcriptional properties. , 1987, Journal of molecular biology.

[9]  R. Britten,et al.  Repetitive and Non-Repetitive DNA Sequences and a Speculation on the Origins of Evolutionary Novelty , 1971, The Quarterly Review of Biology.

[10]  Denis Sereno,et al.  A Common Mechanism of Stage-regulated Gene Expression inLeishmania Mediated by a Conserved 3′-Untranslated Region Element* , 2002, The Journal of Biological Chemistry.

[11]  P. Deininger,et al.  Repeat sequence families derived from mammalian tRNA genes , 1985, Nature.

[12]  David M. A. Martin,et al.  The Genome of the African Trypanosome Trypanosoma brucei , 2005, Science.

[13]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[14]  D. Mosser,et al.  Exploitation of the complement system by Leishmania promastigotes. , 1996, Parasitology today.

[15]  A. Evsikov,et al.  Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. , 2004, Developmental cell.

[16]  G. Glazko,et al.  Origin of a substantial fraction of human regulatory sequences from transposable elements. , 2003, Trends in genetics : TIG.

[17]  G. Matlashewski,et al.  The Developmental Expression of Leishmania donovani A2 Amastigote-specific Genes Is Post-transcriptionally Mediated and Involves Elements Located in the 3′-Untranslated Region* , 1996, The Journal of Biological Chemistry.

[18]  B. E. Kimmel,et al.  Ingi, a 5.2-kb dispersed sequence element from Trypanosoma brucei that carries half of a smaller mobile element at either end and has homology with mammalian LINEs , 1987, Molecular and cellular biology.

[19]  T. Eickbush,et al.  Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition , 1993, Cell.

[20]  J. Jurka,et al.  Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. M. Requena,et al.  Identification of a putative regulatory element in the 3'-untranslated region that controls expression of HSP70 in Leishmania infantum. , 2000, Molecular and biochemical parasitology.

[22]  C. Alonso,et al.  Characterization of a non-long terminal repeat retrotransposon cDNA (L1Tc) from Trypanosoma cruzi: homology of the first ORF with the ape family of DNA repair enzymes. , 1995, Journal of molecular biology.

[23]  Shulamit Michaeli,et al.  MINIREVIEWS trans and cis Splicing in Trypanosomatids : Mechanism , Factors , and Regulation , 2003 .

[24]  Jonathan Bingham,et al.  Visualizing large hierarchical clusters in hyperbolic space , 2000, Bioinform..

[25]  Kim Rutherford,et al.  Artemis: sequence visualization and annotation , 2000, Bioinform..

[26]  Dimitri A Kramerov,et al.  Short retroposons in eukaryotic genomes. , 2005, International review of cytology.

[27]  N. Biteau,et al.  The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei. , 2003, Molecular biology and evolution.

[28]  D Sereno,et al.  A new developmentally regulated gene family in Leishmania amastigotes encoding a homolog of amastin surface proteins. , 2000, Molecular and biochemical parasitology.

[29]  H. Wichman,et al.  SINE extinction preceded LINE extinction in sigmodontine rodents: implications for retrotranspositional dynamics and mechanisms , 2005, Cytogenetic and Genome Research.

[30]  Christian Biémont,et al.  Genetics: Junk DNA as an evolutionary force , 2006, Nature.

[31]  B. Papadopoulou,et al.  Distinct 3′-Untranslated Region Elements Regulate Stage-specific mRNA Accumulation and Translation in Leishmania* , 2005, Journal of Biological Chemistry.

[32]  F. Crick,et al.  Selfish DNA: the ultimate parasite , 1980, Nature.

[33]  J. Brosius,et al.  RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. , 1999, Gene.

[34]  F. Bringaud,et al.  Evolution of non-LTR retrotransposons in the trypanosomatid genomes: Leishmania major has lost the active elements. , 2006, Molecular and biochemical parasitology.

[35]  J. M. Requena,et al.  The Translational Efficiencies of the Two Leishmania infantum HSP70 mRNAs, Differing in Their 3′-Untranslated Regions, Are Affected by Shifts in the Temperature of Growth through Different Mechanisms* , 2005, Journal of Biological Chemistry.

[36]  E. Ullu,et al.  Alu sequences are processed 7SL RNA genes , 1984, Nature.

[37]  J. M. Requena,et al.  The expression of HSP83 genes in Leishmania infantum is affected by temperature and by stage-differentiation and is regulated at the levels of mRNA stability and translation , 2004, BMC Molecular Biology.

[38]  P. Myler,et al.  Evaluation of differential gene expression in Leishmania major Friedlin procyclics and metacyclics using DNA microarray analysis. , 2003, Molecular and biochemical parasitology.

[39]  P. Anderson,et al.  TIA‐1 is a translational silencer that selectively regulates the expression of TNF‐α , 2000 .

[40]  R Braun,et al.  Control of polyadenylation and alternative splicing of transcripts from adjacent genes in a procyclin expression site: a dual role for polypyrimidine tracts in trypanosomes? , 1994, Nucleic acids research.

[41]  F. Bringaud,et al.  Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi. , 2002, Molecular and biochemical parasitology.

[42]  W. Doolittle,et al.  Selfish genes, the phenotype paradigm and genome evolution , 1980, Nature.

[43]  Daniel Nilsson,et al.  Comparative Genomics of Trypanosomatid Parasitic Protozoa , 2005, Science.

[44]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[45]  M. Ouellette,et al.  Adaptation of Leishmania cells to in vitro culture results in a more efficient reduction and transport of biopterin. , 2001, Experimental parasitology.

[46]  C. Clayton,et al.  Life without transcriptional control? From fly to man and back again , 2002, The EMBO journal.

[47]  A. Delcher,et al.  The Trypanosoma cruzi L1Tc and NARTc non-LTR retrotransposons show relative site specificity for insertion. , 2006, Molecular biology and evolution.

[48]  N. Agabian.  Trans splicing of nuclear pre-mRNAs , 1990, Cell.

[49]  P. Overath,et al.  The molecular phylogeny of trypanosomes: evidence for an early divergence of the Salivaria. , 1998, Molecular and biochemical parasitology.

[50]  J. Donelson,et al.  Regulation of genes encoding the major surface protease of Leishmania chagasi via mRNA stability. , 2005, Molecular and biochemical parasitology.

[51]  M. Ouellette,et al.  A combined proteomic and transcriptomic approach to the study of stage differentiation in Leishmania infantum , 2006, Proteomics.

[52]  Sudhir Kumar,et al.  MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment , 2004, Briefings Bioinform..

[53]  D. Labuda,et al.  CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[54]  M. Shapira,et al.  A regulatory role for the 5' and 3' untranslated regions in differential expression of hsp83 in Leishmania. , 1994, Nucleic acids research.

[55]  A. Smit.  Interspersed repeats and other mementos of transposable elements in mammalian genomes. , 1999, Current opinion in genetics & development.

[56]  M. Ouellette,et al.  Protection against Leishmania major challenge infection in mice vaccinated with live recombinant parasites expressing a cytotoxic gene. , 1998, The Journal of infectious diseases.

[57]  J. Jurka,et al.  A novel class of SINE elements derived from 5S rRNA. , 2003, Molecular biology and evolution.

[58]  R. Britten,et al.  Mobile elements inserted in the distant past have taken on important functions. , 1997, Gene.

[59]  J. Bennetzen,et al.  Nested Retrotransposons in the Intergenic Regions of the Maize Genome , 1996, Science.

[60]  M. Shapira,et al.  Expression of heat shock protein 83 in Leishmania is regulated post-transcriptionally. , 1994, Molecular and biochemical parasitology.

[61]  M. Hatzoglou,et al.  Nutritional Control of mRNA Stability Is Mediated by a Conserved AU-rich Element That Binds the Cytoplasmic Shuttling Protein HuR* , 2002, The Journal of Biological Chemistry.

[62]  J. Donelson,et al.  The Genome of the African Trypanosome , 2002 .

[63]  B. Haas,et al.  The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease , 2005, Science.

[64]  C. Clayton,et al.  Hierarchies of RNA-processing signals in a trypanosome surface antigen mRNA precursor , 1994, Molecular and cellular biology.

[65]  J. Shapiro,et al.  Retrotransposons and regulatory suites. , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

[66]  N. Okada,et al.  The 3' ends of tRNA-derived short interspersed repetitive elements are derived from the 3' ends of long interspersed repetitive elements , 1996, Molecular and cellular biology.

[67]  Thierry Heidmann,et al.  LINE-mediated retrotransposition of marked Alu sequences , 2003, Nature Genetics.

[68]  M. Shapira,et al.  Developmental regulation of heat shock protein 83 in Leishmania. 3' processing and mRNA stability control transcript abundance, and translation id directed by a determinant in the 3'-untranslated region. , 2001, The Journal of biological chemistry.

[69]  P. Overath,et al.  The surface structure of trypanosomes in relation to their molecular phylogeny. , 2001, International journal for parasitology.

[70]  T. Holzer,et al.  A Negative Regulatory Element Controls mRNA Abundance of the Leishmania mexicana Paraflagellar Rod Gene PFR2 , 2003, Eukaryotic Cell.

[71]  M. Ouellette,et al.  A novel antifolate resistance gene on the amplified H circle of Leishmania. , 1992, The EMBO journal.

[72]  Daniel Nilsson,et al.  Messenger RNA processing sites in Trypanosoma brucei. , 2005, Molecular and biochemical parasitology.

[73]  R Braun,et al.  Accurate polyadenylation of procyclin mRNAs in Trypanosoma brucei is determined by pyrimidine-rich elements in the intergenic regions , 1994, Molecular and cellular biology.

[74]  Heather J Munden,et al.  The Genome of the Kinetoplastid Parasite, Leishmania major , 2005, Science.