Genome paper Sinorhizonium Meliloti

Database

1. 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])?

The Data can be found in-house in the database. As far as data that can be found on the database it is mostly gene IDs and pathways through the cell but they do have sequencing available, but to my knowledge a lot if not most of it is in french. In order to get the structure, another database is required. The database is a primary database and it is manually updated through a community

2. What individual or organization maintains the database? The organizations that maintain the database are INRA, CNRS, and LIPM (it was listed but the link didn't work)

3. What is their funding source(s)? The funding sources The organizations that maintain the database

4. Is there a license agreement or any restrictions on access to the database? No restrictions or license agreements

1. How often is the database updated?

The database hasn't been updated since 2008

5. Are there links to other databases? There are links to the KEEG database which provides pathways for the genes

6. Can the information be downloaded? Yes, the information can be downloaded

7. In what file formats? As far as I can find, Its only in a text file

Evaluate the “user-friendliness” of the database.

1. Is the Web site well-organized?

yes its well organized but assumes you know how to use it

1. Does it have a help section or tutorial?

No help or tutorial found

1. Run a sample query. Do the results make sense?

yes I can find the gene ID number and links to the gene itself

8. 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_####).

For Sinorhizobium meliloti the id is SMc#### (the numbers change for some reason, though the model organism appears to be SMc1021)

Terms

• Megaplasmid - Genomic material that is not found in the chromosome that contains 100kb or more of information. Usually found in highly diverse species of bacteria
• Root Nudules - Nodes that grow on the plant's roots and are generally linked with Nitrogen fixing symbiosis between the plant and a bacteria
• Endosymbionts - an organism that exhibits symbiosis that lives within the body of another organism
• Replicon - region of DNA or RNA that uses a single origin of replication during transcription
• Paralogous Family - Genes that are considered to have arisen and subsequently differed due to a duplication of genetic material
• ABC transporters- transmembrane proteins that use ATP binding to power the transport of substrates across a barrier.
• Extracytoplasmic function - A function that occurs outside of the cell's cytoplasm
• Ortholog - Genes that are generated after speciation
• Orphan Genes - Genes that only exist in a small group or single organism. They are not found in the rest of the taxonomic tree
• Insertion sequence - Small tranposable genes that only encode for transposon activity

Outline

Overview

• Need for nitrogen Fixation bacteria
  • reduction of dinitrogen to ammonium
• Genome of the Sinorhizobium meliloti
  • 3.65 mb chromosome
  • 1.35 pSymA Megaplasmid
  • 1.68 pSymB megaplasmid
• Study of these 3 genetic carriers can lead to a better understanding of genes related to nitrogen fixation and how they play a role in the soil environment
  • Sustainable agriculture
  • Ecosystem function
• Method of plant interaction

1. Infection of the plant roots
2. Creation of Nodules
3. Fixation of nitrogen by the bacteria
4. Metabolic interplay between the plant and the bacteria

• What still needs to be understood
  • Creation of the organelle in the nodules
  • How the bacterium can safely infect a host without a host response
  • Why the nitrogen fixation to the host instead of its self

Features of the Genome

• overview of the 3 replicons chromosome, pSymA, and pSymB
• Size of all three of the replicons
• Comparison to the Mezorhizobium loti genome
  • Function found for 59.7% of genes

Genetic overview

• 8.2% of genes are unique to S.meliloti
• Not many genes were recently duplicated
• 42% of genes are found in 584 paralogous families
  • genome size has not recently had constraints
  • leads to a more adaptive organism
• insertion sequences
  • 2% of genes
  • mostly on pSymA near genetic material used for symbiosis
  • Shows that symbiotic elements are prone to change

pSym megaplasmids

• Large size blurs the lines between plasmids and chromosomes
• contain ABC transporter genes
• pSymA may be transferable while pSymB is considered non-transferable
• possible extracellular origin for pSymA
• pSymA has no essential genes while pSymB has essetial genes
  • pSymA is Plasmid like and pSymB is considered more chromosomal like

transport functions

• largest class of genes (12%)
• ABC transport
• relative abundance is high on pSymB (17.4%)
• Rht transporters
• No PTS system

Regulatory proteins

• 8.7% of genes
• Most are LysR
  • Especially on pSymA
• GntR regulators found more on megaplasmids
• AsnC regulators found more on Chromosome
• No serine-threonine kinases were detected

Bacterial Adhesion elements

• poorly understood
• T-Pilus system
• Another system that seems to play a role is the host specificity
• LPSs, ESPs, CPSs

Nodule formation

• Nod factors on pSymA
  • 2 nod genes that are highly conserved
• gene paralogs
  • nodG and fabG

Nitrogen Fixation and Metabolism

• larger relative portion of genes on pSymA
• orthologous genes
• no homologous genes found

Energy metabolism and its role in the Symbiosis

• S.meliloti is aerobic
• factors that help S.meliloti conserve and produce energy in low oxygen environments
• Cytochrome c oxidase
• NADH-ubiquinone gene clusters

Comparison of genes to other Rhizobium

• Comparison between S.meliloti and 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
• M.loti has nodule forming genes that are not found in S.meliloti
• Rhizoba that appear similar in function such as M.loti and S.meliloti have a large difference in their genes

Conclusion

• 3 replicons with distinct features
• Hypothesis that the 2 megaplasmids were introduced into the S.meliloti genome separately
• pSymB broadens the metabolic capabilities of S.meliloti
• increased ability at producing polysaccharides
• pSymA aquisition allowed for node formation + ability to function in a low oxygen environment