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==Genome structure==
==Genome structure==


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% (1,075) of the 1,990 ORF consisted of biological role categories, 10.5% (208) of those have an unknown function, 9.2% (184) were conserved hypothetical proteins/domain proteins while the other 26.3% (523) were hypothetical proteins (2). Repetitive elements such as DNA repeats (which include clustered regularly interspaced short palindromic repeats (CRSPRs) and uninterrupted direct repeats) and transposable components (which include insertion sequence (IS) elements and miniature inverted-repeat transposable elements (MITEs)) made up 6% of the whole genome (2). However, the strain did not contain other classes of dispersed repetitive DNA sequence elements which include ERIC and REP elements (2).
The genome size of circular 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 total ORF of 1990 (covered the complete genome by 85%). <sup>[[#References|[11]]]</sup>,<sup>[[#References|[13]]]</sup> 54% of the ORF consisted of biological role categories, 10.5% have an unknown function, 9.2% were conserved hypothetical proteins/domain proteins while the other 26.3% were hypothetical proteins.<sup>[[#References|[11]]]</sup> Repetitive elements such as DNA repeats (clustered regularly interspaced short palindromic repeats and uninterrupted direct repeats) and transposable components (insertion sequence elements and miniature inverted-repeat transposable elements) made up 6% of the whole genome.<sup>[[#References|[11]]]</sup> The strain did not contain other classes of dispersed repetitive DNA sequence elements which include ERIC and REP elements.<sup>[[#References|[11]]]</sup>


==Cell structure and metabolism==


==Cell structure and metabolism==
The cell structure of ''Porphyromonas gingivalis'' consists of capsules, fimbriae, lipopolysaccharide (LPS) and outer membrane proteins. <sup>[[#References|[3]]]</sup> Capsules are important for the initial adherence to the host’s teeth, also is vital to provide resistance to the flow of saliva. <sup>[[#References|[3]]]</sup> In vivo experiment has shown that encapsulated strain of ''P. gingivalis'' is more virulent compared to non-encapsulated strain which only caused local infection when infected in mice. This is because the non-encapsulated strains are more susceptible to phagocytosis or can be easily killed by dendritic cells and macrophages while encapsulated strains are able to modulate the host’s immune response, lowering the production of cytokines interleukin-1 (IL-1), IL-6, and IL-8 by fibroblasts. <sup>[[#References|[14]]]</sup>
 
Fimbriae are thin, about 3-25μm long structures that extend out of bacterial outer membrane.<sup>[[#References|[3]]]</sup> ''P. gingivalis'' expresses two types of fimbriae; fimbrillin (FimA), major and long fimbriae encoded by and Mfa protein, minor and short fimbriae.<sup>[[#References|[3]]]</sup> Fimbriae are important for binding and invasion of host cells, also vital for adherence to various oral molecules such as commensal bacteria (for example streptococci).<sup>[[#References|[15]]]</sup> Other than long and short fimbriae, there are also accessory fimbriae; Fim C, D and E which have a role in matrix proteins binding and interaction with CXC-chemokine receptor 4.
 
Lipopolysaccharides (LPS) is a vital structure of the bacterial outer membrane and usually very large in size, >10kDa.<sup>[[#References|[3]]]</sup> It consists of a distal polysaccharide (O-antigen), a core oligosaccharide and a hydrophobic domain (lipid A or endotoxin) (3). The most inner component, endotoxin has heterogeneous acylation pattern which is dynamic depending on environmental surrounding and is able to affect immune signalling of the host, thus increasing the likelihood of survival.<sup>[[#References|[3]]]</sup> LPS plays a vital role in maintaining the cellular and structural integrity of the bacteria, regulating the entry of hydrophobic molecules and toxic chemicals, also involves in folding and insertion of outer membrane protein.<sup>[[#References|[3]]]</sup> Furthermore, LPS is a key component that leads to periodontitis as it is able to activate the host inflammatory responses, such as the production of IL-1, eventually causing the destruction of periodontal tissue.<sup>[[#References|[16]]]</sup>
 
The cell envelope of ''P. gingivalis'' consists of inner and outer membrane, separated by periplasm containing peptidoglycan layer.<sup>[[#References|[3]]]</sup> The cell membrane acts as a selective barrier that only allows certain substances to enter the cell, hence providing protection to the cell.<sup>[[#References|[3]]]</sup> OM proteins which include lipoproteins and integral proteins involved in most specific recognition processes of the bacteria and also important for the formation of periodontal biofilms.<sup>[[#References|[3]]]</sup> Porins and OmpA-like proteins are the most abundant OM proteins. LptO and PG534 are another examples of OM proteins. LptO is important for O-deacylation of LPS, vital for cell attachment while PG534 is important to increase the activities of gingipains.<sup>[[#References|[3]]]</sup> Gingipains are key components of the cell for taking up nutrients, for example, degrades the host’s haemoglobin to acquire iron and haem, also degrades the host’s albumin serum for obtaining enough carbon and nitrogen source.<sup>[[#References|[17]]]</sup>  Other than that, gingipains involve in degrading the signals of immune response.<sup>[[#References|[18]]]</sup>


Cell wall, biofilm formation, motility, metabolic functions.  
''P. gingivalis'' is found to create a synergistic biofilm with ''Treponema denticola'', forming a symbiotic relationship, particularly for utilization of nutrients and also pathogenicity in periodontal disease.<sup>[[#References|[19]]]</sup> ''P. gingivalis'' is usually found beneath the spirochete layer while T. denticola is mostly observed in the surface layers of subgingival plaque.<sup>[[#References|[19]]]</sup> Compared in monospecies biofilms, the growth of ''P. gingivalis''t is more enhanced in synergistic biofilms as ''T. denticola'' produced an important compound, succinate which facilitates its survival.<sup>[[#References|[19]]]</sup>


==Ecology==
==Ecology==


Aerobe/anaerobe, habitat (location in the oral cavity, potential other environments) and microbe/host interactions.
P. gingivalis is an obligate anaerobe and predominantly found in subgingival sulcus, the space between the free gingiva and the tooth surface.<sup>[[#References|[3]]]</sup>,<sup>[[#References|[20]]]</sup> It is also found in a deep periodontal pocket where the availability of sugar is usually very low, hence for energy production, P.gingivalis is able to ferment amino acids.<sup>[[#References|[3]]]</sup>
 
P. gingivalis is usually a secondary colonizer of a dental plaque and the colonization is mediated by saliva which serves as a platform for its transmission and initial entrance into the oral milieu.<sup>[[#References|[3]]]</sup>,<sup>[[#References|[20]]]</sup> The tooth surfaces which are usually coated with salivary pellicle provides attachment for the bacterial fimbriae to resist salivary flow.<sup>[[#References|[20]]]</sup> Eventually, P. gingivalis can reach the subgingival crevice by proliferation with the help of primary colonizer such as Streptococcus gordonii that serves as a site of attachment.<sup>[[#References|[20]]]</sup> Streptococcus gordonii is a facultative anaerobe which can decrease the oxygen levels permissive for the survival of obligate anaerobic.<sup>[[#References|[20]]]</sup> Other than that, the bacteria are also found in the upper gastrointestinal tract, women with bacterial vaginosis, respiratory tract and colon.<sup>[[#References|[10]]]</sup>  
 
To stay alive in the crevice, the microbe needs to interact with the host’s epithelial cells and neutrophils.<sup>[[#References|[20]]]</sup> P. gingivalis adheres, actively invades and replicates within epithelial cells to prevent recognition and surveillance of the immune system.<sup>[[#References|[20]]]</sup> To survive and persist longer in the host’s epithelial cells, P. gingivalis has the genes that encode for nucleoside diphosphate kinase, an enzyme that suppresses ATP-induced apoptosis, hence preventing epithelial cell apoptosis.<sup>[[#References|[20]]]</sup> Also, by invading the cell, it is able to suppress the production of IL-8 by epithelial cells, leading to suppression or delay of neutrophil influx.<sup>[[#References|[20]]]</sup> P. gingivalis is able to resist to environmental oxidative stress generated by neutrophil and oxidative killing by phagocytes by the role played by proteins rubrerythrin and alkyl hydroperoxide reductase.<sup>[[#References|[21]]]</sup>


==Pathology==
==Pathology==
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==References==
==References==
References examples <b></b>:


1. [https://www.google.ch/patents/US5710039 Porphyromonas gingivicanis strain ATCC 55562]
1. [https://www.google.ch/patents/US5710039 Porphyromonas gingivicanis strain ATCC 55562]
Line 69: Line 78:


12. [https://www.atcc.org/products/all/33277.aspx#generalinformation Porphyromonas gingivalis (Coykendall et al.) Shah and Collins]
12. [https://www.atcc.org/products/all/33277.aspx#generalinformation Porphyromonas gingivalis (Coykendall et al.) Shah and Collins]
13. [https://www.ncbi.nlm.nih.gov/pubmed/10556321 Delcher, A.L. (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res <b>7</b>:4636-4641.]
14. [http://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-10-5 Brunner, J., Scheres, N., El Idrissi, N. B., Deng, D. M., Laine, M. L., van Winkelhoff, A. J. (2010). The capsule of Porphyromonas gingivalis reduces the immune response of human gingival fibroblasts. BMC Microbiol <b>10</b>:5.]
15. [https://www.ncbi.nlm.nih.gov/pubmed/17485350 Amano, A. (2007). Disruption of epithelial barrier and impairment of cellular function by Porphyromonas gingivalis. Front Biosci <b>12</b>:3965–3974.]
16. [https://www.ncbi.nlm.nih.gov/pubmed/16398684 Bartold, P. M., and Narayanan, A.S. (2006). Molecular and cell biology of healthy and diseased periodontal tissues. Periodontology <b>2000</b>:29–49.]
17. [https://www.ncbi.nlm.nih.gov/pubmed/25720118 Veillard, F., Potempa, B., Guo, Y., Ksiazek M., Sztukowska M. N., Houston, J. A., Koneru, L., Nguyen, K and Potempa, J. (2015) Purification and characterisation of recombinant His-tagged RgpB gingipain from Porphymonas gingivalis. Biol Chemist <b>396</b>:377-384.]
18. [https://www.ncbi.nlm.nih.gov/pubmed/11447200 Grenier, D. (2001). Role of gingipains in growth of Porphyromonas gingivalis in the presence of human serum albumin. Infect Immun <b>69</b>: 5166–5172.]
19. [https://www.ncbi.nlm.nih.gov/pubmed/16085371 Yamada, M. (2005). Synergistic biofilm formation by Treponema denticola and Porphyromonas gingivalis. FEMS Microbiol Lett <b>250</b>:271-277.]
20. [https://www.ncbi.nlm.nih.gov/pubmed/19348960 Hajishengallis, G. (2009). Porphyromonas gingivalis–host interactions: open war or intelligent guerilla tactics? Microbes Infect <b>6</b>:637-645.]
21. [https://www.ncbi.nlm.nih.gov/pubmed/9529095 Darveau, R.P. (1998). Local chemokine paralysis, a novel pathogenic mechanism for Porphyromonas gingivalis. Infect Immun <b>66</b>:1660–1665.]


<references/>
<references/>


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

Revision as of 16:39, 22 September 2016

Name Bench ID Date [1]

Classification

Higher order taxa

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

Species

Porphyromonas gingivalis, Strain W83

Description and significance

Porphyromonas gingivalis is a gram-negative, obligate anaerobic, non-motile, non-spore-forming microorganism and is one of the predominant human oral microbiota. [1] This rod-shaped, black-pigmented, asaccharolytic and highly proteolytic bacterium cannot grow in the existence of bile (20%) and on rabbit blood agar plates, they have an average size of diameter below 1.5 μm, living individually from each other. [1],[2] It is often found in a deep periodontal pocket, human subgingival plaque, living along with approximately other >500 species of bacteria. [3]

P. gingivalis is a primary causative pathogen that contributed to a chronic periodontitis, a disease that is characterized by the demolition of tooth-supporting tissues, affecting about 50% of population >30 years of age in the United States and globally, it affects about 10-15% adult populations. [1],[4] The disease usually started as an acute gingival tissue inflammation, but then may advance to a creation of teeth pocket which may cause loss of teeth if it is not treated. [3] Periodontitis is more susceptible among patient acquiring systemic diseases. [5],[6]

Periodontitis has been linked with cardiovascular diseases such as coronary artery disease, heart attack and stroke. [3],[7] Other than periodontitis, P. gingivalis has also been associated with pulpal infection, oral abscesses and it was also detected in women with bacterial vaginosis which may cause burning with urination. [8],[9],[10] The bacteria of virulent strain, W83 was first discovered in the 1950s at Bonn, Germany by H.Werner, obtained from an undocumented oral disease and then in 1960s, it was brought by Madeleine Sebald to The Pasteur Institute. [11] P. gingivalis has been cultured and was available at American Type Culture Collection. [12]

Although there have been numerous studies done to explain the mechanism of virulence factors secreted by P. gingivalis and how they interact with the host, investigating a gene or protein in isolation without considering other molecular networks is not truly insightful because in the actual in vivo environment, the genes may work as a system, hence may interact differently than a single virulence factor to the host cells. Adding to that, rather than working alone, P. gingivalis is also likely to interact with other microbes to survive in the harsh environment of the periodontal pocket. [3] Therefore, further research needs to be performed to improve our understanding of the interaction between periodontal bacteria and host cells at the molecular and cellular level so that effective approaches can be implemented to control the disease caused by this bacterium.

Genome structure

The genome size of circular 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 total ORF of 1990 (covered the complete genome by 85%). [11],[13] 54% of the ORF consisted of biological role categories, 10.5% have an unknown function, 9.2% were conserved hypothetical proteins/domain proteins while the other 26.3% were hypothetical proteins.[11] Repetitive elements such as DNA repeats (clustered regularly interspaced short palindromic repeats and uninterrupted direct repeats) and transposable components (insertion sequence elements and miniature inverted-repeat transposable elements) made up 6% of the whole genome.[11] The strain did not contain other classes of dispersed repetitive DNA sequence elements which include ERIC and REP elements.[11]

Cell structure and metabolism

The cell structure of Porphyromonas gingivalis consists of capsules, fimbriae, lipopolysaccharide (LPS) and outer membrane proteins. [3] Capsules are important for the initial adherence to the host’s teeth, also is vital to provide resistance to the flow of saliva. [3] In vivo experiment has shown that encapsulated strain of P. gingivalis is more virulent compared to non-encapsulated strain which only caused local infection when infected in mice. This is because the non-encapsulated strains are more susceptible to phagocytosis or can be easily killed by dendritic cells and macrophages while encapsulated strains are able to modulate the host’s immune response, lowering the production of cytokines interleukin-1 (IL-1), IL-6, and IL-8 by fibroblasts. [14]

Fimbriae are thin, about 3-25μm long structures that extend out of bacterial outer membrane.[3] P. gingivalis expresses two types of fimbriae; fimbrillin (FimA), major and long fimbriae encoded by and Mfa protein, minor and short fimbriae.[3] Fimbriae are important for binding and invasion of host cells, also vital for adherence to various oral molecules such as commensal bacteria (for example streptococci).[15] Other than long and short fimbriae, there are also accessory fimbriae; Fim C, D and E which have a role in matrix proteins binding and interaction with CXC-chemokine receptor 4.

Lipopolysaccharides (LPS) is a vital structure of the bacterial outer membrane and usually very large in size, >10kDa.[3] It consists of a distal polysaccharide (O-antigen), a core oligosaccharide and a hydrophobic domain (lipid A or endotoxin) (3). The most inner component, endotoxin has heterogeneous acylation pattern which is dynamic depending on environmental surrounding and is able to affect immune signalling of the host, thus increasing the likelihood of survival.[3] LPS plays a vital role in maintaining the cellular and structural integrity of the bacteria, regulating the entry of hydrophobic molecules and toxic chemicals, also involves in folding and insertion of outer membrane protein.[3] Furthermore, LPS is a key component that leads to periodontitis as it is able to activate the host inflammatory responses, such as the production of IL-1, eventually causing the destruction of periodontal tissue.[16]

The cell envelope of P. gingivalis consists of inner and outer membrane, separated by periplasm containing peptidoglycan layer.[3] The cell membrane acts as a selective barrier that only allows certain substances to enter the cell, hence providing protection to the cell.[3] OM proteins which include lipoproteins and integral proteins involved in most specific recognition processes of the bacteria and also important for the formation of periodontal biofilms.[3] Porins and OmpA-like proteins are the most abundant OM proteins. LptO and PG534 are another examples of OM proteins. LptO is important for O-deacylation of LPS, vital for cell attachment while PG534 is important to increase the activities of gingipains.[3] Gingipains are key components of the cell for taking up nutrients, for example, degrades the host’s haemoglobin to acquire iron and haem, also degrades the host’s albumin serum for obtaining enough carbon and nitrogen source.[17] Other than that, gingipains involve in degrading the signals of immune response.[18]

P. gingivalis is found to create a synergistic biofilm with Treponema denticola, forming a symbiotic relationship, particularly for utilization of nutrients and also pathogenicity in periodontal disease.[19] P. gingivalis is usually found beneath the spirochete layer while T. denticola is mostly observed in the surface layers of subgingival plaque.[19] Compared in monospecies biofilms, the growth of P. gingivalist is more enhanced in synergistic biofilms as T. denticola produced an important compound, succinate which facilitates its survival.[19]

Ecology

P. gingivalis is an obligate anaerobe and predominantly found in subgingival sulcus, the space between the free gingiva and the tooth surface.[3],[20] It is also found in a deep periodontal pocket where the availability of sugar is usually very low, hence for energy production, P.gingivalis is able to ferment amino acids.[3]

P. gingivalis is usually a secondary colonizer of a dental plaque and the colonization is mediated by saliva which serves as a platform for its transmission and initial entrance into the oral milieu.[3],[20] The tooth surfaces which are usually coated with salivary pellicle provides attachment for the bacterial fimbriae to resist salivary flow.[20] Eventually, P. gingivalis can reach the subgingival crevice by proliferation with the help of primary colonizer such as Streptococcus gordonii that serves as a site of attachment.[20] Streptococcus gordonii is a facultative anaerobe which can decrease the oxygen levels permissive for the survival of obligate anaerobic.[20] Other than that, the bacteria are also found in the upper gastrointestinal tract, women with bacterial vaginosis, respiratory tract and colon.[10]  

To stay alive in the crevice, the microbe needs to interact with the host’s epithelial cells and neutrophils.[20] P. gingivalis adheres, actively invades and replicates within epithelial cells to prevent recognition and surveillance of the immune system.[20] To survive and persist longer in the host’s epithelial cells, P. gingivalis has the genes that encode for nucleoside diphosphate kinase, an enzyme that suppresses ATP-induced apoptosis, hence preventing epithelial cell apoptosis.[20] Also, by invading the cell, it is able to suppress the production of IL-8 by epithelial cells, leading to suppression or delay of neutrophil influx.[20] P. gingivalis is able to resist to environmental oxidative stress generated by neutrophil and oxidative killing by phagocytes by the role played by proteins rubrerythrin and alkyl hydroperoxide reductase.[21]

Pathology

Application to biotechnology

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

Current research

Summarise some of the most recent discoveries regarding this species.

References

1. Porphyromonas gingivicanis strain ATCC 55562

2. Naito, M., Hirakawa, H., Yamashita, A., Ohara, N., Shoji, M., Yukitake, H., Nakayama, K., Toh, H., Yoshimura, F., Kuhara, S., Hattori, M., Hayashi, T., Nakayama, K. (2008) Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis. DNA Res 4:215-25.

3. How, K.Y., Song, K.P., Chan, K.G. (2016) Porphyromonas gingivalis: An Overview of Periodontopathic Pathogen below the Gum Line. Front Microbiol 7:53.

4. Petersen, P.E., Ogawa, H. (2012) The global burden of periodontal disease: towards integration with chronic disease prevention and control. 60:15-39.

5. Oxidative stress and periodontal disease in Down Syndrome

6. Mehta, A. (2015) Risk factors associated with periodontal diseases and their clinical considerations. Int J Contemp Dent Med Rev.

7. Nakano, K. (2006) Detection of cariogenic Streptococcus mutans in extirpated heart valve and atheromatous plaque specimens. J Clin Microbiol 9:3313-3317.

8. Loos, B.G. (1992) A statistical approach to the ecology of Porphyromonas gingivalis. J Dent Res 71:353-358.

9. Wolff, L.F. (1993) Natural distribution of 5 bacteria associated with periodontal disease. J Clin Periodontol 20:699-706.

10. Charlene, W.J. (2014) Anaerobes and Bacterial Vaginosis in Pregnancy: Virulence Factors Contributing to Vaginal Colonisation. Int J Environ Res Public Health 11:6979-7000.

11. Nelson, K.E. (2003). Complete Genome Sequence of the Oral Pathogenic Bacterium Porphyromonas gingivalisStrain W83. J Bacteriol 185:5591-5601.

12. Porphyromonas gingivalis (Coykendall et al.) Shah and Collins

13. Delcher, A.L. (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 7:4636-4641.

14. Brunner, J., Scheres, N., El Idrissi, N. B., Deng, D. M., Laine, M. L., van Winkelhoff, A. J. (2010). The capsule of Porphyromonas gingivalis reduces the immune response of human gingival fibroblasts. BMC Microbiol 10:5.

15. Amano, A. (2007). Disruption of epithelial barrier and impairment of cellular function by Porphyromonas gingivalis. Front Biosci 12:3965–3974.

16. Bartold, P. M., and Narayanan, A.S. (2006). Molecular and cell biology of healthy and diseased periodontal tissues. Periodontology 2000:29–49.

17. Veillard, F., Potempa, B., Guo, Y., Ksiazek M., Sztukowska M. N., Houston, J. A., Koneru, L., Nguyen, K and Potempa, J. (2015) Purification and characterisation of recombinant His-tagged RgpB gingipain from Porphymonas gingivalis. Biol Chemist 396:377-384.

18. Grenier, D. (2001). Role of gingipains in growth of Porphyromonas gingivalis in the presence of human serum albumin. Infect Immun 69: 5166–5172.

19. Yamada, M. (2005). Synergistic biofilm formation by Treponema denticola and Porphyromonas gingivalis. FEMS Microbiol Lett 250:271-277.

20. Hajishengallis, G. (2009). Porphyromonas gingivalis–host interactions: open war or intelligent guerilla tactics? Microbes Infect 6:637-645.

21. Darveau, R.P. (1998). Local chemokine paralysis, a novel pathogenic mechanism for Porphyromonas gingivalis. Infect Immun 66:1660–1665.


  1. MICR3004

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