Lena Week 11
Contents |
The Genome of the Kinetoplastid Parasite, Leishmania major.
Vocabulary
1.)promastigote: the flagellate stage of a trypanosomatid protozoan, as that of any of the Leishmania parasites.
2.)amastigote: the nonflagellate, intracellular, morphologic stage in the development of certain hemoflagellates, resembling the typical adult form of Leishmania.
3.)phagolysome:a cellular body that is formed by the union of a phagosome or ingested particle with a lysosome that contains hydrolytic enzymes.
4.)macrophage: any of the large, mononuclear, highly phagocytic cells derived from bone marrow cells, promonocytes, the progeny of which, the monocytes, enter the bloodstream, where they stay for a few days before entering the tissues and developing into macrophages. They are components of the monocyte-macrophage system. Macrophages are usually immobile but become actively mobile when stimulated by inflammation, immune cytokines and microbial products. They are an important class of antigen presenting cells (APCs).
5.)glycoconjugate: any of the complex molecules containing glycosidic linkages, such as glycolipids, glycopeptides, oligosaccharides, or glycosaminoglycans.
6.)aneuploid: Having a chromosome number that is not a multiple of the haploid number for the species.
7.)pseudogene:a defective segment of DNA that resembles a gene but cannot be transcribed.
8.)ortholog: any gene found in two or more species that can be traced to a common ancestor; specif. one of two homologous genes that is descended from a common ancestor, but which has evolved in a different way.
9.)synteny: the presence of two or more genes on the same chromosome.
10.)trypanosome: any minute, flagellate protozoan of the genus Trypanosoma, parasitic in the blood or tissues of humans and other vertebrates, usually transmitted by insects, often causing serious diseases, as African sleeping sickness in humans, and many diseases in domestic animals.
11.)proteolytic: the breaking down of proteins into simpler compounds, as in digestion.
Significance
Leishmania is a pathogenic parasite that causes range a diseases in humans--these maladies are collectively termed the leishmaniases. Each year, approximately 2 million people across 88 countries are infected with leishmaniases. This paper looked at the genome of Leishmania major, paying particular attention to molecular processes such as chromatin remodeling, transcription, RNA processing, translation, posttranslational modification, and protein turnover. Leishmania in particular has distinctive surface glycoconjugates that are essential to its host-parasite interactions. The synthesis of these molecules was examined. These processes were compared against the related species Trypanasoma brucei and Trypanasoma cruzi. In the article, these three species are referred to as the 'tritryps.' Leishmania major's sequenced genome has given insight to how it functions as a parasite, and may be useful in developing therapies to treat Leishmania infections. Additionally, the comparison of Leishmania major to 'Trypanasoma brucei and Trypanasoma cruzi allows evolutionary biologists to look at eukaryote evolution, and the genetic divergences between the three Trypanosomatids studied.
Methods
The researchers used shot-gun sequencing. Shot gun sequencing breaks up DNA into many fragments, then sequences them into what are called reads. A researcher would perform this several times to get many reads, then a computer uses the overlapping ends of reads to generate a full and continuous sequence. In this project, large-insert clones and purified chromosomal DNA were shotgun sequenced. This allowed them to generate a full sequence for each of Leishmania's 36 chromosomes. The genome sequence was determined on a chromosome-by-chromosome basis. The sequences were then compared to an optical map to ensure accuracy. Additionally, the Leishmania genome was analysis with the help of algorithms to predict numbers of RNA genes, pseudogenes, and protein-coding genes.
Results and Discussions
- Algorithms predict Leishmania species to have 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes.
- 36% of these genes are thought to have a function.
- 3083 of Leishmania's genes form 662 putative related-gene families.
- Small gene families (fewer than 10 members) are thought to have arisen from tandem gene duplication.
- Larger gene families have multuple loci that code for single genes and/or tandem arrays.
- Below is Table 1 from the paper, which summarized the Leishmania genome.
Genome Structure and Content
- The ends of each Leishmania major chromosome contain a previously reported tripartite "repeated-repeat" structure.
- Many of the genes sequenced for "Leishmania" have orthologs in Trypanosoma brucei and Trypanosoma cruz (closely related members of the order Typanasomatid), however 910 Leishmania major genes have no orthologs in either species.
- 74 groups are orthologous for L. major: and T. brucei.
- 482 groups are orthologous for L. major and T. cruzi.
- Some of the "Leishmania restricted" genes are responsible for key metabolic differences between Leishmania and the other tritryps.
- As much as 68% of "Leishmania restricted" genes have unknown functions.
RNA Processing
- Regulation of splicing probably appeared early in eukaryotic evolution.
- Degredation of mRNAs is important to regulation of tritryp gene expression.
- The presence of tripanosomatid genes for transcriptional regulation indicates that tritryps rely on post-transcriptional control of gene expression.
Translation and co-/post-translational modification
- Most of the major components of translation are found in tritypes with numbers similar to those observed in lower eukaryotes.
- There is, however, expansion of the eIF-4A genes, which suggests more specialization in the tritryps.
- Protein modification follows the typical eukaryotic processes: phosphorylation, glycosylation, and lipidation.
- Essential modifications observed in the tritryps include glycosylphosphatidylinositol-anchor addtion, acylation, prenylation.
- These modifications alls facilliate membrane attachments and/or protein-protein interactions.
- Essential modifications observed in the tritryps include glycosylphosphatidylinositol-anchor addtion, acylation, prenylation.
Surface Molecules
- The surface of the Leishmania major parasite is distinctive due to the presence of a number of glycoconjugates, which are involved in various aspects of its infection cycle.
- These include: lipophosoglycan (LPG), glycoinositolphospholipids (GIPLs), membrane proteophosphoglycan (PPG), and glycosylated GPI anchored proteins.
- The secreted acid phosphatase and other PPGs contain postranslational modifications and vary in structure, expression, and function among different species of Leishmania.
Proteolysis
- Peptidases represent approximately 2% of protein-coding genes in the tritryps (this is true in most eukaryotes.)
- Some of these peptidases have been identifies as virulence factors, vaccine candidates, and drug targets.
- Trypanosomatids are the only known eukaryotes with both a proeasome and a eubacterial HslVU complex.
- Trypanosomatids also have several ubiquitin-conjugating enzymes, which indicates an active nonlysosomal cytosolic protein degradation system.
- The tritryps contain several metacaspases, which is consistant with a caspase-independent cell death mechanism.
- None of the ~200 mammalian peptidase inhibitors were found in the tritryps, but tritryps encode inhibitors of cysteine peptidase which mammals lack.
- Leishmania's inhibitors of cysteine peptidase may be important in host-parasite interaction.
- Tritryps also encode inhibitors of serine peptidases (normally found only in a few bacterial species.)
- Serine peptidases are abundant in mammals and insects (both susceptiable to L. major infection) and it is probably that inhibitors of serine peptidases are important to host-parasite interactions.
Model Organism Database
Database: http://tritrypdb.org/tritrypdb/getDataset.do?question=GeneQuestions.GenesByTaxon&display=detail#61
- The Database provides links to identify genes, identify genomic sequences, and identify isolates. It is a meta-database and is curated manually by a community.
- The database in maintained by the EuPathDP Scientific working group with Scientific advisors for Leishmania: Richard Burchmore from University of Glasgow, Barbara Papadopoulou from Laval University, Jeremy Mottram from University of Glasgow, and Angela Cruz from Universidade de São Paulo.
- They are funded by the Bill and Melinda Gates Foundation and by the Wellcome Trust.
- There are no access restrictions to the database. It is open to the public as long as they cite the database.
- The database is updated as new research arises, but not on a regular basis. It was last updated on September 25th, 2013.
- There are links to GeneDB.
- The information is not downloadable.
- The interface is not very user-friendly. There is no help section or tutorial. If you know exactly what you are searching for, there are links to click on, but if you are just browsing it is not inviting. The sample query seemed to make sense.
- The gene format is for Leishmania major LmjF.##.####
