Blitvak Week 11

Initial Project Work

Work done on 11/10

• A possible MOD covering B. cenocepacia was found: Burkholderia Genome Database
• A test search was conducted for 'Burkholderia cenocepacia J2315

11/12

• The possible MOD was accessed and a test search was conducted:

• It was noticed that most "locus tags" were in the format BCAL####
• Some of the tags included an A at the end
• It was noticed that instead of BCAL, some genes were BCAM or BCAS
• Another test search was performed to observe the total number of genes with an ID that begins with "BCA":

• • This searched yielded 7341 records (potentially, 7341 different genes)
• A similar search was conducted using the term "BCAL", which should cover all of genes with IDs that start with "BCAL"
  • This search yielded 3603 records
• Another search was done using "BCAM"
  • This search yielded 2859 records
• A search was done which covered the term "BCAS"
  • This search yielded 779 records
• The last three searches were summed, yielding 7241 records (100 are unaccounted for)
• An advanced search was done in order to find the 100 records with an unknown starting pattern:

• • It was found that the last 100 records started with pBCA (100 results, only)
  • In this last search, it was noticed that most of the tags only had 3 numbers and that some ended with a lowercase a
• Reviewing the website, it was noticed that "%" is interpreted as wildcard by the database. A search was then done using the term "BCA%a" in order to see the number of records that ended with an "A"; it was noticed that some of these results included a lower-case r before the numbers (looking at the other columns in the search result, such as "Product name", it was realized that the tags that included the r corresponded to genes encoding for different types of tRNA (which correspond to the different amino acids)
• In the latest news section of the database it was stated that there is an updated beta version of the MOD available (http://beta.burkholderia.com/); this updated website will be used in future work

Preparation for Genome Paper Presentation

Unfamiliar Biology Terms from the Manuscript

• Saprophyte: An organism that absorbs, feeds upon, or grows upon decaying organic matter or waste (matter could be originally from animal or plant sources)
  • Citation: [1]
• Orthologous gene/Ortholog: A gene that is found within two or more species that likely originated within a common ancestor (the genes, if orthologous, can be traced back to a common ancestor)
  • Citation: [2]
• CDSs: abbreviated form of "coding sequences" (the region of DNA that is actually transcribed and translated to protein or functional RNA)
  • Citation: [3]
• Replicon: Unit of DNA that contains a DNA replication origin, a termination point, and the potential for self-replication OR a linear or circular segment of DNA/RNA which replicates (sequentially) as a unit
  • Citation: [4]
• Concatenation (in relation to genetics): The joining of two DNA fragments (in a lab, physically, or in software)
  • Citation: [5]
• Genomic Island: Gene clusters that likely originated due to horizontal gene transfer (>8 kb in size) in bacterial/archaeal genomes. Genomic islands encode for genes that are notable adaptations with environmental and medical interest (these genes play an important role in the evolution, or population change, of such microbes with the islands)
  • Citation: [6]
• Mobile genetic elements: small mobile sequences of DNA which can replicate and insert themselves at random sites within chromosomes (also known as a transposon). In bacteria, MGEs come in simple (only code for the genes needed for insertion) and complex (contains genes in addition to what's needed for insertion) forms.
  • Citation: [7]
• Rearrangement: Structural change of a chromosome that leads to a change in the loci order
  • Citation: [8]
• Prophage: Genome of a lysogenic bacteriophage that has come to be incorporated into the chromosome of the bacterial host (prophage is replicated along with the host chromosome)
  • Citation: [9]
• Efflux system: An active transport system (localized in the cytoplasmic membrane) with the purpose of moving substrate in and out of a bacterial cell (e.g. antibiotics)
• Peritrichous: Related to cilia/appendage organs projecting from around the cell; uniform distribution of flagella over a cell
  • Citation: [10]
• Fimbrial: Short filamentous projection in a bacterial cell that is used for adherence to other bacterial cells or to animal cells (not for motility)
  • Citation: [11]

Article Outline

Link to Article: http://jb.asm.org/content/191/1/261.long

Importance of the work

• B. cenocepacia is a very clinically relevant part of the B. cepacia complex (BCC), which is a group of hardy (high degree of antibiotic resistance) gram-negative bacteria that typically reside in water or soil (18 different species, with some being plant or human pathogens). B. cenocepacia is an opportunistic pathogen which causes lung infections in CF (cystic fibrosis) patients; infection by B. cenocepacia is extremely difficult to treat due to a high level of antibiotic resistance, and thus, infection is tied to increased levels of mortality and a decline in the functioning of the lung. The manuscript covered the genome of B. cenocepacia J2315, which is a member of a recently emerged (1990s) epidemic lineage of B. cenocepacia that was extremely transmissible (especially between people with CF); this epidemic lineage is known as the ET12 epidemic strain, that is a part of the IIIA subgroup of B. cenocepacia (subgroups were found, phylogenetically, through the analysis of the recA gene). IIIA strains, unlike those associated with the other subgroups, are rarely encountered in a natural environment, suggesting that the strains have strongly adapted to a host-associated pathogen lifestyle (versus that of a soil saprophyte). There also exist many virulence markers that are encountered more frequently with IIIA strains than with other subgroups; the ET12 isolates, additionally, are known to have a cable pilus which permits binding to molecules within the host environment, such as mucins (which are abundant in the lung). J2315, specifically, is an isolate derived from a CF patient and it exhibits strong levels of antibiotic resistance; it is a member of the ET12 lineage which is a part of the IIIA subgroup. The value of the genomic analysis of J2315 lies in the fact that it will give some elucidation regarding the factors responsible for the success of the strain (via CF patient infection); genomic analysis will also help explain how the members of the ET12 lineage adapted, recently, to holding a niche via human infection (instead of holding a niche in the soil, as a soil saprophyte). In short, J2315 represents a unique and extremely significant pathogen in the realm of CF treatment as it possesses properties that allow it thrive even further in the lung environment than other related strains/subgroups; genomic analysis will produce something that will serve as an essential resource for future investigations into J2315 and the disease that is caused by Burkholderia cenocepacia.