Difference between revisions of "Genome paper Sinorhizonium Meliloti"

Revision as of 03:01, 12 November 2013

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