Genome paper Sinorhizonium Meliloti
From LMU BioDB 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
- Infection of the plant roots
- Creation of Nodules
- Fixation of nitrogen by the bacteria
- 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