Stephen Louie Week 11
From LMU BioDB 2013
Contents |
Note
Apologies for the late terms and database. Accidentally created an outline and presentation for the Microarray paper.
Terms
- Induce:to cause (something) to happen or exist
- Source:[Merriam-Webster]
- Replicon:a linear or circular section of DNA or RNA which replicates sequentially as a unit
- Source:[Merriam-Webster]
- Plasmid:an extrachromosomal ring of DNA especially of bacteria that replicates autonomously
- Source:[Merriam-Webster]
- Mb:mega base pairs = 1,000,000 bp
- Source:[Wikipedia]
- α-probacterium:a class of Proteobacteria. Proteobacteria are a major group (phylum) of bacteria.
- Source:[Wikipedia]
- Paralogy:shared ancestry caused by a gene duplication event in the genome.
- Source:[Wikipedia]
- Biosynthesis:the production of a chemical compound by a living organism
- Source:[Merriam-Webster]
- Orthologs:genes in different species that originated by vertical descent from a single gene of the last common ancestor.
- Source:[Wikipedia]
- Endosymbionts:any organism that lives within the body or cells of another organism, i.e. forming an endosymbiosis.
- Source: [Wikipedia]
- Orphan genes:a gene that has limited phylogenetic distribution. This also means that these genes lack detectable homology to organisms outside such phylogenetic distribution.
- Source: [Wikipedia]
Outline
The Composite Genome of the Legume Symbiont Sinorhizobium meliloti
- Plant growth is reliant on the availability of usable nitrogen.
- Most nitrogen can only be found in soil or fertilizer.
- Rhizobia: aerobic gram-negative soil bacteria
- When plants are deprived of nitrogen, rhizobia are capable of establishing nitrogen-fixing symbiosis.
- Rhizobia infect roots to form root nodules. The bacteria then undergo nitrogen-fixation within the cell cytoplasm.
- Rhizobia and plant exchange signals during this process. The rhizobia continue to provide nitrogen to plant in exchange for plant carbon compounds
- Evolution in legumes has shown the ability to obtain nitrogen from rhizobia while growing in poor soils.
- Sinorhizobium meliloti: the rhizobia symbiont to alfalfa
- As an α-probacterium it is closely related to bacterial plant and animal pathogens
- Some topics of interest include: how microbe stimulates nodule formation, how it manages to invade plant without triggering immune system defenses, how and why microbe fixes nitrogen for the host as opposed to itself, and how bacterium maintains itself within the soil environment.
- Extensive genetic, biochemical, and metabolic research have already been done on it making it an ideal subject for genomic investigation.
- Sinorhizobium meliloti strain 1021 has been fully sequenced.
- The Sinorhizobium meliloti genome consists of three replicons
- One large replicon of 3.65 Mb and two smaller replicons pSymA (1.35 Mb) and pSymB (1.68 Mb).
- Genome is not highly repeated (A limited number of genes seem to be recently duplicated)
- 42% (2589) of Sinorhizobium meliloti genes belong to 548 paralogous families ranging from 2-134 genes per family.
- High paralogy levels indicate that genome size had very little limitation during its evolution. This means that the bacterium was able to gain new adaptive functions for living in the soil and plant-symbiosis.
- Insertion sequence and phage sequences compose 202% of genome with overall abundance on pSymA, particularly near symbiotic genes. This enforces the idea that symbiotic regions are subject to DNA rearrangements.
- The unusual size of pSymA and pSymB makes them difficult to determine whether they are plasmids or chromosomes.
- pSymA was shown to contain putative conjugate transfer genes traACDG and a putative oriT sequence found on other Rhizobial plasmids.
- Essential genes are found to be present on pSymB, showing it to be more chromosome-like.
- Genes encoding for transport systems compose the largest (12%) class of genes in the Sinorhizobium meliloti genome.
- Most of these (17.4%) are found on pSymB. Thus, pSymB is shown to be important for transporting small molecules.
- Regulatory genes make up 8.7% of the Sinorhizobium meliloti genome. The LysR family is prevalent on pSymA.
- Each replicon has a distinct regulatory gene profile.
- Sinorhizobium meliloti ecodes the most nucleotide cyclases of any bacterial genome
- It is not well known how rhizobia connect to plant hair.
- Surface polysaccharides (especially exopolysaccharides) are crucial for plant infection by suppressing the immune system of the plant.
- 12% of pSymB genes have been predicted to be involved with polysaccharide biosynthesis.
- Two new loci were found on the chromosome and nine on pSymB.
- Nodulation genes are found on pSymA
- Two well preserved duplications of nod genes in the genome were found. nodM is suggested to be recently duplicated from glmS.
- Sequence analysis hints that the origins of Sinorhizobium meliloti nod genes are either resident gene duplication or horizontal gene transfer mediated by import of pSymA from an unknown bacterium.
- Nitrogen metabolism is a major feature encoded by the Sinorhizobium meliloti genome, especially in pSymA.
- Only 9 nif genes were found in the genome. Most if not all of these genes were found on pSymA.
- pSymA also carries glutamate dehydrogenase, a subset of genes that are required for denitrification and nitrate transport.
- High levels of energy are necessary for Sinorhizobium meliloti to maintain nitrogen-fixation while in a low oxygen environment in the nodule.
- Both pSymA and the chromosome have been shown to carry a large NADH-ubiquinone dehydrogenase gene cluster that may enhance energy metabolism in symbiosis.
- Genome of Sinorhizobium meliloti was compared to the genome of M. loti
- 35% of M.loti genes had no ortholog in S. meliloti
- Megaplasmid genes in S. meliloti were spread out in the M. loti
- Aside from nitrogen-fixing and nodule forming genes, M. loti has no orthologs in S. meliloti
- Determination of S. meliloti 1021 shows that it has a composite structure consisting of three unique replicons of different architecture and service features.
- This is consistent with the hypothesis that both megaplasmids were inherited from an ancestor with a single chromosome.
- Acquirement of pSymB has increased the metabolic capacity considerably.
- Acquirement of pSymA also led to ability to nodulate, colonize low-oxygen environment of nodules, and metabolize nitrogen compounds under various chemical forms.
- Complete genome sequence allows for opportunities to study the rhizobium-legume symbiosis and the nitrogen-fixation mechanisms of these bacteria.
Molecular Organism Database
Database [Sinorhizobium meliloti 1021 Genome Page]
- The website provides information on the genome sequence attributes, organism taxonomy, and DNA molecule numerical data. Due to lack of funding, the database is curated on a ad hoc basis.
- J. Craig Venter Institute maintains the database
- The website is currently without direct funding. It is being partially funded by a Microbial Sequence Center (MSC) grant from the National Institute of Allergy and Infectious Diseases (NIAID)
- All information is publicly available
- There is no schedule of updates. The database was last updated 2 years ago
- Links are provided to the GenBank FTP, JCVI FTP, Sequencing Center Genome Page, NCBI Genome Page, and the Publication page
- The information can be downloaded in the tab delimited or MySQL format.
- The site is well-organized. There is a tutorial section. The sample query makes sense as long as you have an idea what the name of your organism is
- The format (regular expression) of the main type of gene ID for Sinorhizobium meliloti is simply "Sinorhizobium meliloti 1021"
Genome Presentation
File:Sinorhizobium Meliloti.pdf
