Larry Simpson | University of California, Los Angeles (original) (raw)
Papers by Larry Simpson
Proceedings of the National Academy of Sciences
Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis
Cold Spring Harbor Monograph Archive, 1982
Proceedings of the National Academy of Sciences of the United States of America, Mar 3, 1998
Molecular and Biochemical Parasitology, 1989
We have isolated a 0.3-kb HaeIII restriction fragment from Trypanosoma brucei which contains two ... more We have isolated a 0.3-kb HaeIII restriction fragment from Trypanosoma brucei which contains two tRNA genes. Secondary structure models predict that the two genes identified encode tRNA molecules which specify glycine (anticodon UCC) and leucine (anticodon CAG). The two genes are separated by 86 nucleotides, transcribed in the same direction and contain features of conventional RNA polymerase III transcription units. Southern blot analysis indicates the presence of multicopy tRNa gene families in T. brucei.
Molecular and Biochemical Parasitology, Oct 31, 1995
Rna, Nov 1, 1995
The previously observed extensive sequence heterogeneity of the kinetoplast minicircle DNA in Try... more The previously observed extensive sequence heterogeneity of the kinetoplast minicircle DNA in Trypanosoma cruzi, both intra- and interstrain, has raised the question as to how the minicircle DNA in this species can have any guide RNA (gRNA)-coding capacity at all, because there do not appear to be any variable-region sequences conserved between different strains. To address this question, we obtained the complete edited sequence of maxicircle unidentified reading frame 4 mRNA and identified 25 cognate gRNAs from gRNA libraries constructed from two clonal strains of T. cruzi--Sylvio X10/CL1 and CAN III/CL1. Libraries of PCR-amplified minicircle-variable regions were also constructed for both strains. A single gene for each gRNA was identified in the same polarity within specific minicircle-variable regions from both strains, 60-100 nt downstream from the conserved 12mer sequence. GTP-capped total gRNA from one strain failed to cross-hybridize with minicircle DNA from the other strain. The explanation for this proved to be the number of polymorphisms, mainly transitions, within the homologous gRNAs in the two strains. In most cases, these transitions did not destroy the edited mRNA/gRNA base pairing, as a result of the allowed G-U wobble base pairing. The sequences of the variable regions containing homologous gRNAs in the two strains probably derived from an ancestral sequence, and each has accumulated sufficient polymorphisms so as not to allow hybridization. Within a strain, multiple redundant gRNAs were identified that encode identical editing information but have different sequences.
Molecular and Biochemical Parasitology, May 1, 1989
Molecular and Biochemical Parasitology, Jun 30, 1995
Meth Enzymology, 1996
ABSTRACT The kinetoplastid protozoa, together with the euglenoids, represent one of the earliest ... more ABSTRACT The kinetoplastid protozoa, together with the euglenoids, represent one of the earliest branches of eukaryotes containing mitochondria. There are two major subgroups within the Kinetoplastida: the bodonids–cryptobiids and the trypanosomatids. This chapter focuses on trypanosomatids. Members of the trypanosomatid genera Trypanosoma and Leishmania are the causal agents of several important diseases in humans and animals, including visceral and dermal leishmaniasis, South American Chagas disease, and African sleeping sickness. These digenetic species have a biphasic life cycle that involves both a vertebrate host and an invertebrate vector. Species belonging to the monogenetic genera Crithidia, Blastocrithidia, Leptomonas, and Herpetomonas parasitize only invertebrates. Most species can be grown axenically, and, in some cases, both stages of the life cycle can be maintained.
Mitochondrion, 2015
We studied the intramitochondrial localization of several multiprotein complexes involved in U-in... more We studied the intramitochondrial localization of several multiprotein complexes involved in U-insertion/deletion RNA editing in trypanosome mitochondria. The editing complexes are located in one or two antipodal nodes adjacent to the kinetoplast DNA (kDNA) disk, which are distinct from but associated with the minicircle catenation nodes. In some cases the proteins are in a bilateral sheet configuration. We also found that mitoribosomes have a nodal configuration. This type of organization is consistent with evidence for protein and RNA interactions of multiple editing complexes to form an ~40S editosome and also an interaction of editosomes with mitochondrial ribosomes.
PLoS neglected tropical diseases, 2015
U-insertion/deletion RNA editing is a post-transcriptional mitochondrial RNA modification phenome... more U-insertion/deletion RNA editing is a post-transcriptional mitochondrial RNA modification phenomenon required for viability of trypanosomatid parasites. Small guide RNAs encoded mainly by the thousands of catenated minicircles contain the information for this editing. We analyzed by NGS technology the mitochondrial genomes and transcriptomes of two strains, the old lab UC strain and the recently isolated LEM125 strain. PacBio sequencing provided complete minicircle sequences which avoided the assembly problem of short reads caused by the conserved regions. Minicircles were identified by a characteristic size, the presence of three short conserved sequences, a region of inherently bent DNA and the presence of single gRNA genes at a fairly defined location. The LEM125 strain contained over 114 minicircles encoding different gRNAs and the UC strain only ~24 minicircles. Some LEM125 minicircles contained no identifiable gRNAs. Approximate copy numbers of the different minicircle classes...
Proceedings of the National Academy of Sciences
Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis
Cold Spring Harbor Monograph Archive, 1982
Proceedings of the National Academy of Sciences of the United States of America, Mar 3, 1998
Molecular and Biochemical Parasitology, 1989
We have isolated a 0.3-kb HaeIII restriction fragment from Trypanosoma brucei which contains two ... more We have isolated a 0.3-kb HaeIII restriction fragment from Trypanosoma brucei which contains two tRNA genes. Secondary structure models predict that the two genes identified encode tRNA molecules which specify glycine (anticodon UCC) and leucine (anticodon CAG). The two genes are separated by 86 nucleotides, transcribed in the same direction and contain features of conventional RNA polymerase III transcription units. Southern blot analysis indicates the presence of multicopy tRNa gene families in T. brucei.
Molecular and Biochemical Parasitology, Oct 31, 1995
Rna, Nov 1, 1995
The previously observed extensive sequence heterogeneity of the kinetoplast minicircle DNA in Try... more The previously observed extensive sequence heterogeneity of the kinetoplast minicircle DNA in Trypanosoma cruzi, both intra- and interstrain, has raised the question as to how the minicircle DNA in this species can have any guide RNA (gRNA)-coding capacity at all, because there do not appear to be any variable-region sequences conserved between different strains. To address this question, we obtained the complete edited sequence of maxicircle unidentified reading frame 4 mRNA and identified 25 cognate gRNAs from gRNA libraries constructed from two clonal strains of T. cruzi--Sylvio X10/CL1 and CAN III/CL1. Libraries of PCR-amplified minicircle-variable regions were also constructed for both strains. A single gene for each gRNA was identified in the same polarity within specific minicircle-variable regions from both strains, 60-100 nt downstream from the conserved 12mer sequence. GTP-capped total gRNA from one strain failed to cross-hybridize with minicircle DNA from the other strain. The explanation for this proved to be the number of polymorphisms, mainly transitions, within the homologous gRNAs in the two strains. In most cases, these transitions did not destroy the edited mRNA/gRNA base pairing, as a result of the allowed G-U wobble base pairing. The sequences of the variable regions containing homologous gRNAs in the two strains probably derived from an ancestral sequence, and each has accumulated sufficient polymorphisms so as not to allow hybridization. Within a strain, multiple redundant gRNAs were identified that encode identical editing information but have different sequences.
Molecular and Biochemical Parasitology, May 1, 1989
Molecular and Biochemical Parasitology, Jun 30, 1995
Meth Enzymology, 1996
ABSTRACT The kinetoplastid protozoa, together with the euglenoids, represent one of the earliest ... more ABSTRACT The kinetoplastid protozoa, together with the euglenoids, represent one of the earliest branches of eukaryotes containing mitochondria. There are two major subgroups within the Kinetoplastida: the bodonids–cryptobiids and the trypanosomatids. This chapter focuses on trypanosomatids. Members of the trypanosomatid genera Trypanosoma and Leishmania are the causal agents of several important diseases in humans and animals, including visceral and dermal leishmaniasis, South American Chagas disease, and African sleeping sickness. These digenetic species have a biphasic life cycle that involves both a vertebrate host and an invertebrate vector. Species belonging to the monogenetic genera Crithidia, Blastocrithidia, Leptomonas, and Herpetomonas parasitize only invertebrates. Most species can be grown axenically, and, in some cases, both stages of the life cycle can be maintained.
Mitochondrion, 2015
We studied the intramitochondrial localization of several multiprotein complexes involved in U-in... more We studied the intramitochondrial localization of several multiprotein complexes involved in U-insertion/deletion RNA editing in trypanosome mitochondria. The editing complexes are located in one or two antipodal nodes adjacent to the kinetoplast DNA (kDNA) disk, which are distinct from but associated with the minicircle catenation nodes. In some cases the proteins are in a bilateral sheet configuration. We also found that mitoribosomes have a nodal configuration. This type of organization is consistent with evidence for protein and RNA interactions of multiple editing complexes to form an ~40S editosome and also an interaction of editosomes with mitochondrial ribosomes.
PLoS neglected tropical diseases, 2015
U-insertion/deletion RNA editing is a post-transcriptional mitochondrial RNA modification phenome... more U-insertion/deletion RNA editing is a post-transcriptional mitochondrial RNA modification phenomenon required for viability of trypanosomatid parasites. Small guide RNAs encoded mainly by the thousands of catenated minicircles contain the information for this editing. We analyzed by NGS technology the mitochondrial genomes and transcriptomes of two strains, the old lab UC strain and the recently isolated LEM125 strain. PacBio sequencing provided complete minicircle sequences which avoided the assembly problem of short reads caused by the conserved regions. Minicircles were identified by a characteristic size, the presence of three short conserved sequences, a region of inherently bent DNA and the presence of single gRNA genes at a fairly defined location. The LEM125 strain contained over 114 minicircles encoding different gRNAs and the UC strain only ~24 minicircles. Some LEM125 minicircles contained no identifiable gRNAs. Approximate copy numbers of the different minicircle classes...