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The genome size of strain W83 (GenBank: AE015924.1) is 2,343,479 bp containing 4 ribosomal operons (5S-23S-tRNAAla-tRNAIle-16S), 2 structural RNA genes and 53 specific amino acid tRNA genes, with an average G+C content of 48.3% and having a total ORF of 1990 (covered the complete genome by 85%) (1-2). 54% of ORF consisted of biological role categories, 10.5 % of those have an unknown function, 9.2% were conserved hypothetical proteins/domain proteins while 26.3 were hypothetical proteins (2).  
The genome size of strain W83 (GenBank: AE015924.1) is 2,343,479 bp containing 4 ribosomal operons (5S-23S-tRNAAla-tRNAIle-16S), 2 structural RNA genes and 53 specific amino acid tRNA genes, with an average G+C content of 48.3% and having a total ORF of 1990 (covered the complete genome by 85%) (1-2). 54% of ORF consisted of biological role categories, 10.5 % of those have an unknown function, 9.2% were conserved hypothetical proteins/domain proteins while 26.3 were hypothetical proteins (2).  


[[File:sc.png|List of encoded gene in genome of strain W83|500px]] [[File:sc2.png|List of encoded gene in genome of strain W83|500px]]
[[File:sc.png|List of encoded gene in genome of strain W83|500px]]             [[File:sc2.png|List of encoded gene in genome of strain W83|500px]]





Revision as of 15:54, 5 September 2016

Muhammad Irfan Zulkifle Bench E 1/9/2016 [1]

Classification

Higher order taxa

Bacteria (Kingdom) – FCB Group (Domain) – Bacteroidetes (Phylum) – Bacteroidia (Class) – Bacteroidales (Order) – Porphyromonadaceae (Family) – Porphyromonas (Genus)

Species

  • Porphyromonas gingivalis
  • Type strain: strain 2561 = ATCC 33277= CCUG 25893 = CCUG 25928 = CIP 103683 = DSM 20709 = JCM 12257 = NCTC 11834 [1]

Species name and type strain (consult LPSN http://www.bacterio.net/index.html for this information)

Description and significance

Give a general description of the species (e.g. where/when was it first discovered, where is it commonly found, has it been cultured, functional role, type of bacterium [Gram+/-], morphology, etc.) and explain why it is important to study this microorganism. Examples of citations [2], [3]

File:Microbiata
Table:The predominant human oral microbiota.Porphyromonas gingivalis is one of them

Genome structure

Select a strain for which genome information (e.g. size, plasmids, distinct genes, etc.) is available.

strain: ATCC33277 (less virulent strain)

The size of genome ATCC 33277 (GenBank: AP009380.1) is 2 354 886 bp, consisted of a single circular chromosome containing 2090 CDSs (average size 970bp which covered 86.1% of the complete sequence) and having an average G + C content of 48.4%. The strain has 4 RNA operons (rrn, 5S rRNA-23S rRNA-tRNAAla-tRNAIle-16S rRNA) and 53 specific amino-acid tRNA genes.

Some of the encoded genes:

GenBank (dpp11 gene): BR000944.1 Size: 2,163 bp Topology: Linear

GenBank (mfa2 gene): AB360435.1 Size: 975 bp Topology: Linear

GenBank (fimA(I) gene): AB261608.1 Size: 8,048 bp Topology: Linear

GenBank (ustA gene): AB188568.1 Size: 487bp Topology: Linear

GenBank (fimX gene): AY656999.1 Size: 943 bp Topology: Linear

GenBank (pgmA gene): AY633704.1 Size: 1,473bp Topology: Linear

GenBank (htpG gene): AF176245.1 Size: 2,076 bp Topology: Linear

GenBank (dnaK operon genes): AB015879.1 Size: 9,878 bp Topology: Linear

GenBank (mfa1 gene): AB016284.1 Size: 1,769 bp Topology: Linear

GenBank (pga67 gene): AB006481.1 Size: 2,100 bp Topology: Linear

strain: W38 (virulent strain)

The genome size of strain W83 (GenBank: AE015924.1) is 2,343,479 bp containing 4 ribosomal operons (5S-23S-tRNAAla-tRNAIle-16S), 2 structural RNA genes and 53 specific amino acid tRNA genes, with an average G+C content of 48.3% and having a total ORF of 1990 (covered the complete genome by 85%) (1-2). 54% of ORF consisted of biological role categories, 10.5 % of those have an unknown function, 9.2% were conserved hypothetical proteins/domain proteins while 26.3 were hypothetical proteins (2).

List of encoded gene in genome of strain W83 List of encoded gene in genome of strain W83


Cell structure and metabolism

Cell wall, biofilm formation, motility, metabolic functions.

Ecology

Aerobe/anaerobe, habitat (location in the oral cavity, potential other environments) and microbe/host interactions.

Pathology

Do these microorganisms cause disease in the oral cavity or elsewhere?

The mode of action of Porphyromonas gingivalis

Application to biotechnology

Bioengineering, biotechnologically relevant enzyme/compound production, drug targets,…

Current research

Summarise some of the most recent discoveries regarding this species.

References

References examples

1. List of prokaryotic names with standing in nomenculture

2. Sahm, K., MacGregor, B.J., Jørgensen, B.B., and Stahl, D.A. (1999) Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slotblot hybridization in a coastal marine sediment. Environ Microbiol 1: 65-74.

3. Human Oral Microbiome

  1. MICR3004

This page is written by Muhammad Irfan Zulkifle for the MICR3004 course, Semester 2, 2016