Mpetredi Week 11
From LMU BioDB 2013
Contents |
Mitchell Petredis
[[Team Name]]
NOTE: This assignment will be delayed due to accidentally working on this assignment using the Microarray paper. I will finish the correct outline for the genome paper as soon as possible.
References
Galibert, F., Finan, T.M., Long, S., Puhler, A., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti Science 293:668-672
Unfamiliar Biological Terms (Combination of Genome and Microarray Paper Terms)
- Mb: mega base pairs, equal to 1,000,000 base pairs
- Source: [Wikipedia]
- orphan gene: A strict definition of the term is that no homologous gene exists in any other species. A more liberal definition is that orphan genes are protein-coding regions that have no recognizable homolog in distantly related species
- Source: [Wikipedia]
- kinase: any of various enzymes that catalyze the transfer of phosphate groups from a high-energy phosphate-containing molecule (as ATP) to a substrate
- Source: [Merriam-Webster]
- megaplasmid: Megaplasmids are extrachromosomal genetic elements in the size range of 100 kb and larger. They are found in physiologically and phylogenetically diverse groups of bacteria and archaea. By definition, megaplasmids are not essential for the viability of their hosts under all growth conditions, but paradoxically many megaplasmids carry the genetic information for the defining and characteristic traits of the organism in which they reside.
- Source: [Springer]
- quorum sensing: A phenomenon where microorganisms communicate and coordinate their behavior by the accumulation of signaling molecules. A reaction occurs when a substance accumulates to a sufficient concentration. This is most commonly seen in bacteria.
- Source: [Reference.md]
- nodulation: the process of forming nodules and especially root nodules containing symbiotic bacteria
- Source: [Merriam-Webster]
- rhizophere: soil that surrounds and is influenced by the roots of a plant
- Source: [Merriam-Webster]
- minimal medium: a medium that contains only inorganic salts, a simple carbon source (as carbon dioxide or glucose), and water
- Source: [Merriam-Webster]
- chaperone: any of a class of proteins (as heat shock proteins) that facilitate the proper folding of proteins by binding to and stabilizing unfolded or partially folded proteins
- Source: [Merriam-Webster]
- filamentation: the anomalous growth of certain bacteria, such as E. coli, in which cells continue to elongate but do not divide (no septa formation)
- Source: [Wikipedia]
- chemotaxis: orientation or movement of an organism or cell in relation to chemical agents
- Source: [Merriam-Webster]
- sigma factor: a detachable polypeptide subunit of RNA polymerase that facilitates the initiation of transcription by recognizing specific DNA promoter sites
- Source: [Merriam-Webster]
- periplasm: the region in a gram-negative bacterium between the plasma membrane and an outer surrounding membrane that contains especially enzymes and a thin layer of peptidoglycan
- Source: [Merriam-Webster]
- downregulation: the process of reducing or suppressing a response to a stimulus; specifically : reduction in a cellular response to a molecule (as insulin) due to a decrease in the number of receptors on the cell surface
- Source: [Merriam-Webster]
- plasmolysis: shrinking of the cytoplasm away from the wall of a living cell due to outward osmotic flow of water
- Source: [Merriam-Webster]
- replicon: a linear or circular section of DNA or RNA which replicates sequentially as a unit
- Source: [Merriam-Webster]
Outline of Genome Paper
- Introduction
- Plant growth limited by lack of usable nitrogen.
- Legumes obtain fixed nitrogen compounds due to metabolic association with rhizobial bacteria, powered by photosynthesis
- High protein content in seeds by legumes in poor soil (low nitrogen) conditions may be due to evolution of rhizobia-legume symbiosis
- How Rhizobia work
- Infect roots to form root nodules.
- undergo nitrogen-fixation within the plant cytoplasm.
- Rhizobia and plant exchange signals during this process.
- rhizobia create a flow of bacterial fixed nitrogen for plant carbon compounds
- Symbiotic mechanisms are not clearly understood.
- Much research has been done on S. meliloti in genetics, biochemistry, and metabolic research, making it an ideal specimen to investigate
- General Features of the Genome
- S. meliloti genome has 3 replicons
- 3.65 Mb (Mega Base-Pairs)
- 1.35 Mb for pSymA
- 1.68 Mb for pSymB
- One of the largest genomes at 6.7 Mb and 6204 protein-coding genes, but smaller than M. Loti, which is 7.6 Mb and 6752 protein-coding genes.
- 42% (2589) S. meliloti genes are part of 548 paralogous families, with 2 to 134 genes per family.
- suggests genome size has barely been constrained during S. meliloti evolution and created new adaptive functions for life in soil and symbiosis.
- 2.2% of S. meliloti genome consists of insertion sequence elements and phage sequences.
- 42% (2589) S. meliloti genes are part of 548 paralogous families, with 2 to 134 genes per family.
- S. meliloti genome has 3 replicons
- Replication, transfer, and maintenance of pSym megaplasmids
- unclear if megaplasmids are really plasmids or chromosomes since its sizes are so big
- pSymA does not have an essential gene that could be predicted
- plasmidlike
- pSymB does have essential genes such as arginine tRNA
- chomosomal feature similarity
- Transport functions
- 12% class of genes involve encoding transport systems
- Most are ABC transporters
- 17.4% found on pSymB as import systems for small molecules
- 12% class of genes involve encoding transport systems
- Regulatory proteins
- 8.7% of S. meliloti genome
- Bacterial adhesion and surface structural elements
- poorly understood process
- What is known
- 1 putative adhesin
- 2 agglutin-like genes
- 1 ABC transporter
- up to 12% pSymB could be involved with polysaccharide biosynthesis
- 2 new loci on chromosome
- 9 on pSymB
- functions are yet to be determined and how they interact to specific environmental factors
- Nodulation
- synthesize and export Nod factors
- only found on pSymA
- researchers found 2 very conserved duplications of nod genes within the genome
- nodM = 99% identical (nucleotide sequence level) to glmS and encodes D-glucosamine synthetase
- suggests derivation from duplication of glmS
- nodPQ found in each megaplasmid
- 99% conserved at nucleotide level
- involved in activation of sulfate to 3'-phospoadenosine 5'-phosphosulfate for sulfating of Nod factors in S. meliloti
- Vestiges of IS element next to pSymA copy of nodPQ hints that the copy came from transposition of ancestral pSymB copy
- 99% conserved at nucleotide level
- nodG = paralog of housekeeping chromosomal fabG
- nodM = 99% identical (nucleotide sequence level) to glmS and encodes D-glucosamine synthetase
- main message: S. meliloti nod genes came from 2 distinct origins
- horizontal gene transfer by mediation import of pSymA of an unknown bacteria
- resident gene duplication
- Nitrogen Fixation and nitrogen metabolism
- prominent feature of S. meliloti, especially in pSymA
- 9 nif genes in S. meliloti genome
- all located in pSymA (except nifS ortholog on chromosome and possibly nifV as well)
- no homologs in S. meliloti
- 9 nif genes in S. meliloti genome
- pSymA has glutamate dehydrogenase (necessary for denitrification)
- pSymB encodes…
- nitrate reductase
- 2 nitrate transporters
- single glutamine synthetase (glnII)
- prominent feature of S. meliloti, especially in pSymA
- Energy metabolism in relation to symbiosis
- S. meliloti = aerobic bacterium
- must produce high levels of energy to support nitrogen fixation in low-oxygen environments
- pSymA and Chromosome have large NADH-ubiquinone dehydrogenase gene clusters that possibly enhances energy metabolism in symbiosis
- S. meliloti = aerobic bacterium
- Comparison of S. meliloti genome to other rhizobial genomes
- S. meliloti vs. M. loti
- 35% M. loti genes do not have orthologs in S. meliloti
- genetic info of pSymA and pSymB in S. meliloti is dispersed in M. loti genome
- MAFF303099 symbiotic island in M. loti contains the following
- nodulation genes
- nitrogen fixation genes
- genes w/o orthologs in S. meliloti genome
- unclear if different isolates of a specific species will show high degree of genetic diversity
- more research is required to figure out if conserved and varying genes relate to adaptations for particular plant rhizopheres, environmental conditions, or unknown adaptations
- S. meliloti vs. M. loti
Model Organism Database
Link: http://cmr.jcvi.org/tigr-scripts/CMR/GenomePage.cgi?org=ntsm01
- Types of data: genome sequence attributes, organism taxonomy, DNA molecule numerical data; curation: ad hoc basis.
- Database maintained by J. Craig Venter Institute
- No major funding, but partially funded by a Microbial Sequence Center (MSC) grant from the National Institute of Allergy and Infectious Diseases (NIAID)
- No license agreement or restrictions; free to the public
- No info on frequency of database updates, but it was last updated 2 years ago
- Links:
- GenBank FTP
- JCVI FTP
- Sequencing Center Genome Page
- NCBI Genome Page
- Publication page
- Information available to download in tab delimited or MySQL formats
- Well-organized website and easily accessible.
- Tutorial section is available.
- Sample query results make sense.
- Sinorhizobium meliloti 1021
