Laurmagee: Week 11

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms.
   • symbiont: an organism living in symbiosis; especially the smaller member of a symbiotic pair.
   • a-proteobacterium: a class of the group proteobacteria.
   • tripartite: made between or involving three parties.
   • endosymbionts: symbiosis in which a symbiont dwells within the body of its symbiotic partner.
   • organogenesis: the origin and development of bodily organs.
   • rhizosphere: soil that surrounds and is influenced by the roots of a plant
   • plasmid: extrachromosomal ring of DNA especially of bacteria that replicates autonomously.
   • putative: commonly accepted or supposed.
   • asparagine: a nonesstential amino acid that is an amide of aspartic acid.
   • cyclases: an enzyme that catalyzes.
   • All of the definitions were found: In Merriam Webster Online, Retrieved November 11, 2013, from http://www.merriam-webster.com/dictionary.
2. Write an outline of the article.
   • Nitrogen is often found in soil and fertilizer and it is essential for proper plant growth.
   • When a plant is deprived of necessary nitogen, rhizobia infect the roots of the plant to create nodules. The bacteria then begin nitrogen-fixation in the cell cytoplasm. This establishes a symbiotic relationship between the rhizobia and the plant, where the plant is provided with nitrogen and the rhizobia receive plant carbon compounds.
   • The genome of Sinorhizobium meliloti is being studied, because it serves as a rhizobia symbiont to alfalfa and can offer incite on how other endosymbionts function.
   • Sinorhizobium meliloti is classified as a a-probacterium that is also closely related to bacterial plant and animal pathogens. Sprain 1021 of Sinorhizobium meliloti has been completely sequenced.
   • The genome of interest consists of three replicons: one large replicon of 3.65 Mb, a smaller replicon (pSymA) of 1.35 Mb, and another small replicon (pSymB) of 1.68 Mb.
   • The genes of Sinorhizobium meliloti are not highly repeated, but almost half of them are related to different family classification ranging from 2-134 genes per family. This high of paralogy levels suggest that S. meliloti has had very few limitations during its evolution allowing it to adapt new functions to better suit its environment.
   • Phage sequences comprise about 2.02% of the entire genome, and are more concentrated on pSymA and symbiotic regions. This aligns with the theory that symbiotic regions are subject to DNA rearrangements.
   • pSymA and pSymB are unusually large plasmids, so it is difficult to determine whether they are truly plasmids or are actually chromosomes.
   • pSymA has two different types of putative genes that are characteristic of plasmids, whereas pSymB has been shown to have more chromosome-like genes.
   • Most of the genes responsible for small molecule transport are found on pSymB and pSymA has been related to the LysR family. When regulatory genes are addressed, each replicon is seen as having their own unique regulatory gene profile and S. meliloti as a whole encodes for more nucleotide cyclases than any other bacterial genome sequenced to date.
   • As previously mentioned, S. meliloti infects plant when they are not able to get enough nitrogen from their soil directly. To infect the plant, surface polysaccharides are essential, because they suppress the immune system of the plant. 12% of pSymB is involved with this polysaccharide biosynthesis.
   • Looking further in pSymA, we see that there are genes that illicit nodule formation in the plant. Two duplications were found in the pSym sequence related to nod genes and others have been suggested to be duplicates as well. The presence of these genes in primarily pSymA, offer support to the idea that gene duplication or horizontal gene transfer imported the genes of pSymA from an unknown bacterium.
   • pSymA has also been found to encode genes involved in nitrogen metabolism. Only 9 nifs are found in the entire genome to relate to this function and almost all of these are located on pSymA. In addition, pSymA also carries glutamate dehrdrogenase, which is necessary for denitrification and nitrate transport.
   • Both the chromosome and pSymA contain a cluster of genes involved in enhancing energy metabolism during symbiosis. This is important for S. meliloti particularly, because it has to maintain nitrogen fixation even in soil that is low in oxygen.
   • The genome of S. meliloti was compared to that of M. loti and results suggested that 35% of M. loti genes had no ortholog in S. meliloti. In addition, megaplasmid genes in S. meliloti were more spread out in the M. loti genome.M. loti and S. meliloti did however have similar nitrogen-fixing and nodule forming genes.
   • All of the information provided in the paper was conducive to the conclusion that there are three replicons in the S. meliloti genome. Two of which are megaplasmids that are suspected to have been inherited from familial ancestors. The addition of these plasmids allowed for advantages functionality relating to the symbiotic processes S. meliloti is connected to.
   • The complete sequence genome is helpful in that more can be studied regarding rhizobium-legume symbiosis and mechanisms of nitrogen fixation.
3. What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?
   • There are numerous genome tools available for Sinorhizobium meliloti including a coordinate search, sequence retrieval search, gene retrieval search using coordinates, and finally a region comparison search bar. In addition, there are comparative tools in the database and comprehensive diagrams.
4. What individual or organization maintains the database?
   • The J. Craig Venter Institute is responsible for maintaining the database.
5. What is their funding source(s)?
   • The funding for the database is not noted anywhere on the cite.
6. Is there a license agreement or any restrictions on access to the database?
   • All of the information included in the database is available to the public, therefore, there doesn't appear to be any license agreements or restrictions to the data.
7. How often is the database updated?
   • The last update of the database was in 2011, so it has not been updated for quite sometime.
8. Are there links to other databases?
   • There do not appear to be any links to other databases.
9. Can the information be downloaded? In what file formats?
   • Yes the information can be downloaded into .txt formats.
10. Evaluate the “user-friendliness” of the database. Is the Web site well-organized? Does it have a help section or tutorial? Run a sample query. Do the results make sense?
    • There is a tutorial available on the cite, but my main problem with the database is that it loads very slowly. At first I thought it was my internet connection, or lack there of, causing the database to run slowly, but then I was able to load other windows very quickly in comparison.
11. What is the format (regular expression) of the main type of gene ID for this species? (for example, for Vibrio cholerae it was VC#### or VC_####).
    • SMc#### is the format of gene ID in the database.