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2. LITERATURE REVIEW
The present review overview of what is known to date about Non proteobacteria in
general, such as its taxonomy and biology, with special emphasis on pathogenesis and
the morphological virulence factors involved in pathogenesis.
2.1 Classification of Non-Proteo gram Infectious Negative Bacteria
The class of Non-proteobacteria, which forms one of the largest groups within
bacteria of gram-negative bacteria, contains different phylum like Spirachaete,
Chlamydiaceae, Bacteroidetes, Fusobacteria etc. and it gives different order of nonproteobacteria . It causes different infectious disease in different species of nonproteobacteria. No unique morphological, molecular or biochemical characteristic has
been identified that can distinguish members of the class Non-proteobacteria or its
main orders from other bacteria. Although non-proteobacteria are among the most
extensively studied bacterial groups, they are presently defined solely on the basis of
their clustering and branching pattern in phylogenetic trees.4
Table-1. Classification of Gram-negative non-proteobacterial (Infectious)
Infectious diseases · Bacterial diseases: non-proteobacterial Gram Negative
Treponema
Treponema pallidum (Syphilis/Bejel, Yaws) ·
Treponema carateum (Pinta) · Treponema denticol
Borrelia burgdorferi/Borrelia afzelii (Lyme disease
Spirochaetaceae
Erythema chronicum migrans, Neuroborreliosis)
Borrelia
Spirochaete
Borrelia recurrentis (Louse borne relapsing fever)
Borrelia hermsii/Borrelia duttoni/Borrelia parkeri
(Tick borne relapsing fever)
Leptospiraceae
Leptospira Leptospira interrogans (Leptospirosis)
Spirillaceae
Spirillum Spirillum minus (Rat-bite fever/Sodoku)
Chlamydiaceae Chlamydophila Chlamydophila psittaci (Psittacosis) · Chlamydophila
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pneumoniae
Chlamydia
Bacteroidetes
Chlamydia trachomatis (Chlamydia, Lymphogranuloma
venereum, Trachoma)
Bacteroides fragilis · Bacteroides forsythus · Capnocytophaga canimorsus ·
Porphyromonas gingivalis · Prevotella intermedia
Fusobacterium necrophorum (Lemierre's syndrome) · Fusobacterium
Fusobacteria
nucleatum · Fusobacterium polymorphum
Streptobacillus moniliformis (Rat-bite fever/Haverhill fever)
2.2.1 Spirochaete
Spirochaetes / Spirochetes belong to a phylum of distinctive diderm (doublemembrane) bacteria, most of which have long, helically coiled (spiral-shaped) cells.
They are chemoheterotrophic in nature, with lengths between 0.1 µm and diameters
around 0.1 to 0.6 µm. Spirochaetes are distinguished from other bacterial phyla by
the location of their flagella, sometimes called axial filaments, which run lengthwise
between the bacterial inner membrane and outer membrane in periplasmic space.
These cause a twisting motion which allows the spirochaete to move about. When
reproducing, a spirochaete will undergo asexual transverse binary fission.
The spirochaetes are divided into three families, Brachyspiraceae, Leptospiraceae
and Spirochaetaceae, all placed within a single order, Spirochaetales. Diseasecausing members of this phylum include the following:
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Leptospira species, which causes leptospirosis
Borrelia burgdorferi, B. garinii, and B. afzelii, which cause Lyme disease
Borrelia recurrentis, which causes relapsing fever
Treponema pallidum subspecies pallidum, which causes syphilis
Treponema pallidum subspecies pertenue, which causes yaws
Brachyspira pilosicoli and Brachyspira aalborgi, which cause intestinal
spirochetosis
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Cavalier-Smith has postulated that the Spirochaetes belong in a larger clade called
Gracilicutes.
Fig: 2 Spirochaete
2.2.2 Chlamydiaceae
Chlamydiaceae is a family of bacteria that belongs to the Phylum Chlamydiae, Order
Chlamydiales. All Chlamydiaceae species are Gram-negative and express the familyspecific lipopolysaccharide epitope αKdo-(2→8)-αKdo-(2→4)-αKdo (previously
called the genus-specific epitope). All Chlamydiaceae ribosomal RNA genes have at
least 90% DNA sequence identity. Chlamydiaceae species have varying inclusion
morphology, varying extrachromosomal plasmid content, and varying sulfadiazine
resistance. Chlamydiaceae currently includes two genera and one candidate genus:
Chlamydia, Chlamydophila and Candidatus Clavochlamydia.
Species C. trachomatis, C. muridarum, and C. suis all belong to Chlamydia genera. C.
trachomatis has been found only in humans, C. muridarum in hamsters and mice
(family Muridae), and C. suis in swine. Chlamydia spp. produces a small amount of
detectable glycogen and has two ribosomal operons.
C. trachomatis is the cause of a Chlamydia infection commonly transmitted sexually
(often referred as just "Chlamydia") and also causes trachoma, an infectious eye
disease, spread by eye, nose, and throat secretions.
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Fig:3 Chlamydiaceae
2.2.3 Bacteroidetes
The phylum Bacteroidetes is composed of three large classes of Gram-negative,
nonsporeforming, anaerobic, and rod-shaped bacteria that are widely distributed in the
environment, including in soil, in sediments, sea water and in the guts and on the skin
of animals.
By far, Bacteroidia are the most well-studied class, including the genus Bacteroides
(an abundant organism in the feces of warm-blooded animals including humans), and
Porphyromonas, a group of organisms inhabiting the human oral cavity. The class
Bacteroidia, was formally called Bacteroidetes as it was until recently the only class
in the phylum; the name has been changed in the fourth volume of ―Bergey's Manual
of Systematic Bacteriology‖.
Members of the genus Bacteroides are opportunistic pathogens. This phylum is
sometimes grouped with Chlorobi, Fibrobacteres, Gemmatimonadates, Caldithrix
and Marine group A to form the FCB group or superphylum. In the alternative
classification system proposed by Cavalier-Smith, these taxa are a class in the
Sphingobacteria phylum.
Fig4: Bacteroidetes
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2.2.4
Fusobacteria
Fusobacteria are obligately anaerobic non-sporeforming gram-negative bacilli. Since
the first reports in the late nineteenth century, various names have been applied to
these organisms, sometimes with the same name being applied to different species.
More recently, not only have there been changes to the nomenclature, but also
attempts to differentiate between species which are believed to be either pathogenic or
commensal or both. Because of their asaccharolytic nature (incapable of metabolizing
carbohydrates), and a general paucity of positive results in routine biochemical tests,
laboratory identification of the fusobacteria has been difficult. However, the
application of novel molecular biological techniques established a number of new
species, together with the subspeciation of Fusobacterium necrophorum and F.
nucleatum, and provided new methods for identification. The involvement of
fusobacteria in a wide spectrum of human infections causing tissue necrosis and
septicaemia has long been recognised, and more recently, their importance in intraamniotic infections, premature labour and tropical ulcers has been reported.
Since the first reports of fusobacteria in the late nineteenth century, the variety of
species names has led to some confusion within the genera Fusobacterium and
Leptotrichia. However, newer methods of investigation have led to a better
understanding of the taxonomy. Among the new species described are F. ulcerans
from tropical ulcers, and several species from the oral cavity. Subspeciation of the
important species F. necrophorum and F. nucleatum has also been possible. It is
probable that the taxonomy of the fusobacteria may be further developed in the future.
Fig:5 Fusobacteria
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2.2 Nonproteobacteria: Worldwide Distribution
Worldwide distribution of gram-negative non-proteobacteria causes different disease
on the basis of phylum or order of bacteria such as; Spirochaete bacteria cause Lyme
disease, Syphilis and Intestinal Spirochaetosis. These infectious disease caused by
different genus of Spirochetes in many country or some are distributed in worldwide.
Borrelia burgdorferi causes Lyme disease in Western United States, Northeastern and
Midwest. Especially in Canda, Europe, South or North America, Japan, China,
Thailand and northern Africa .
Treponema pallidum is a species of spirochaete bacterium that causes syphilis.
Syphilis is believed to have infected 12 million people worldwide in 1999, with
greater than 90% of cases in the developing world . Syphilis was very common is
Europe during the 18th and 19th centuries. In the developed world during the early
20th century, infections declined rapidly with the widespread use of antibiotics, until
the 1980s and 1990s . Since the year 2000, rates of syphilis have been increasing in
the USA, UK, Australia and Europe, primarily among men who have sex with men.
Increased rates among heterosexuals have occurred in China and Russia since the
1990s. .
Brachyspira is a genus of bacteria classified within the phylum of spirochetes. It
causes intestinal spirochaetosis in pigs so that disease is widespread in pig-rearing
countries. But it has also been isolated from dogs, birds and mice. It causes zoonotic
infection in humans, with infection thought to originate from dogs . The combination
of homosexuality and HIV infection has been shown to further increase the risks of
clinical intestinal spirochaetosis in citizens of Western countries like the USA,
Germany , Australia, France and worldwide.
Species of Fusobacteria causes Periodontal disease, Rat bite fever and Haverhill
fever. Fusobacterium nucleatum is an oral bacterium, indigenous to the human oral
cavity, that plays a role in periodontal disease Rat bite fever can be found Worldwide
Research has emerged implicating periodontal disease caused by Fusobacterium
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nucleatum with preterm births in humans. It is present in larger amounts in adults than
in children and in diseased sites than in healthy sites .
Streptobacillus moniliformisis the causative agent of rat bite fever in North and South
America while a different organism, Spirillum minus, is primarily responsible for this
disease in Asia and other countries. Most cases occur in Japan, but specific strains of
the disease are present in the United States, Europe, Australia, and Africa .
Bacteroidetes are opportunistic pathogens. Bacteroides fragilis is involved in 90% of
anaerobic peritoneal infection. Bacteroidetes fragilis is the most prevalent organism
in the Bacteroidetes group, accounting for 41% to 78% of the isolates of the group.
The Bacteroides fragilis group is the species of Bacteroidaceae that is isolated with
greatest frequency in clinical specimens.It causes disease worldwide .
Porphyromonas gingivalis is anaerobic pathogenic bacterium and implicated in
certain forms of periodontal disease, upper gastrointestinal tract, respiratory tract etc
and linked to Rheumatoid arthritis and it is occurred many countries
Capnocytophaga Canimorsus is gram-negative bacillus bacterium that causes a
zoonotic disease, most commonly in aslepnic patients. It causes fulminant sepsis with
disseminated intravascular coagulation. Species of Chlamydiae causes Pneumonia,
bronchitis, pharyngitis, sinusitis, myocarditis, ocular trachoma, pelvic inflammatory
disease or other infectious disease.
Chlamydia trachomatis causes significant infection and disease Worldwide. In United
States, Chlamydia trachomatis is the most common sexually transmitted bacterial
pathogen and major cause of pelvic inflammatory disease an estimated 3 million
Chlamydia trachomatis infection occur annually in the United States. Another disease
caused by this organism, ocular trachoma, affects 500million people, with 7 to 9
million of those infected becoming blind. Lymphogranuloma venereum is sexually
transmitted disease that is unusual in Europe and North America but relatively
frequent in Africa, Asia and South America . Chlamydia cause inflammatory
conjunctivitis disease and mostly in Egypt, North Africa .
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Chlamydophila psittaci is an endemic pathogen of all bird species and causes
pneumonia. Psittacine bird (e.g. Parrots, parakeets) are major reservoir for human
disease, but outbreaks have occurred among turkey-processing workers and pigeon
aficionados . It causes disease worldwide .
The TWAR strain was first isolated from the conjunctiva of a child in Taiwan. It was
initially considered to be a psittacosis strain, because the inclusions produced in cell
culture resembled those of Chlamydophila psittaci. The Taiwan isolate (TW-183)
was shown to be serologically related to a pharyngeal isolate (AR-39) isolated from a
college student in the United states, and thus the new strain was called ―TWAR‖, an
acronym for TW and AR(acute respiratory). To date, only this one this one serotype
of the new species, Chlamydophila pneumonia, has been identified. Chlamydophila
pneumonia causes pneumonia, bronchitis, pharyngitis, sinusitis and flulike illness . It
causes all of these disease in worldwide
2.3 Structure Morphology
Morphological characterization study is also important because it gives characteristics
of bacterial and that is important in pathogenesis differentiation. For example: In case
of Treponema, Pathogenic strains have a capsule-like outer coat that is not present in
non-pathogenic strains.. Apart from morphological variations among disease causing
bacteria focus is given on the genes and proteins having important role in
pathogenesis
Complete genome sequence of an organism can be considered to be the ultimate
genetic map, in the sense that the heritable characteristics are encoded within the
DNA and that the order of all the nucleotides along each chromosome is known.
However, knowledge of the DNA sequence does not tell us directly how this genetic
information leads to the observable traits and behaviors (phenotypes) that we want to
understand. Finding all the functional parts of genome sequences and using this
information to improve the health of individuals and society are the focus of the next
phase of the Human Genome Project. Comparative analyses of genome sequences
will be a major part of this effort.
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Comparative analysis of the protein products encoded in complete genomes provides
a powerful tool for evaluating evolutionary trends and adaptive strategies in
pathogenic microbes.
Identification of metabolic and signaling pathways that are unique to pathogens offers
novel targets for therapeutic intervention. Also, such unique determinants may prove
useful in developing better diagnostic and prognostic indicators of infectious diseases
in humans. Conclusions from such an analysis enhance understanding of the hostparasite interactions that enable pathogens to carve out unique ecological niches in
nature.
2.4 Role of Outer Membrane Protein in Pathogenesis
Outer membrane protein(omp) and Phenylalanyl-tRNA (PheT) gene and protein are
studied in this research work because both of that genes are present in all of selected
nonproteobacteria. So it may be helpful for vaccine production for preventing disease.
Nonproteobacteria possesses an outer membrane characteristics of gram-negative
bacteria and generally most of the bacteria conatin outer membrane protein(OMPs). It
is assumed that components of the outer membrane, among which are proteins, are
involved in the pathogenesis of infection of gram-negative bacteria. The OMPs can
function as receptors for phages and mitogens and act as specific substrate binding
sites. Some OMPs are pores that are important for transport of nutrients and some are
involved in coaggregation between bacteria.
It has been demonstrated that OMPs of gram-negative bacteria can be involved in
invasion of tissue and that surface-exposed loops of OMPs are of importance for
virulence. OMPs may serve as antigens and have been considered for the production
of vaccines. For example in Fusobacterium nucleatum peridontal disease. As per the
genetic level thereby also gaining better knowledge of the structure and functions of
the outer membrane proteins. OMPs are of great interest with
respect to
coaggregation, cell nutrition and antibiotic susceptibility. Several studies have shown
that OMPs are involved in the pathogenicity of gram-negative bacteria.
A recombinant Outer surface protein A vaccine has been licensed for use in humans
against Lyme disease caused by infection with organisms belonging to the Borrelia
Burgdorferi complex . The vaccine Lymerix is a lapidated recombinant outer surface
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protein that derived from Borrelia burgdorferi. Although many issues surrounding
vaccine use remain unsettled, the vaccine is expected to be in widespread use in
endemic areas. Infection is also prevented by avoiding tick-infested areas; wearing
protective clothing; checking your clothing, body and pets of ticks; and removing
them promptly. There is no vaccines against infections caused by other Borrelia
species .
In July 2007, Construction and immunogenicity of recombinant adenovirus
expressing the major outer membrane protein (MOMP) of Chlamydophila psittaci in
chicks.The first study explores the use of the major outer membrane protein encoded
by the outer membrane protein gene, as a candidate for a vaccine against avian
chlamydiosis. Pathogen free chicks were inoculated. Detection through an indirect
hemagglutination test showed that these chicks generated antibodies against the major
outer membrane protein of Chlamydophila psittaci. 9 out of 10 vaccinated chicks
were protected from the disease when challenged, whereas the control groups showed
clinical signs of the disease when challenged. This study shows that the major outer
membrane protein gene of Chlamydophila psittaci may serve as a candidate vaccine
against avian chlamydiosis. Bacteroidetes is also an opportunistic pathogen and
causes disease. No vaccine is also available for preventing disease.
2.5 Pathogenicity based on Grams Nature and Outemembrane proteins
Fig:6 Cell wall of Gram Negative Bacteria
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Outer Membrane
Both gram-positive and gram-negative bacteria have a cell wall made up of
peptidoglycan and a phospholipid bilayer with membrane-spanning proteins.
However, gram-negative bacteria have a unique outer membrane, a thinner layer of
peptidoglycan, and a periplasmic space between the cell wall and the membrane. In
the outer membrane, gram-negative bacteria have lipopolysaccharides (LPS), porin
channels, and murein lipoprotein all of which gram-positive bacteria lack.
As opposed to gram-positive cells, gram-negative cells are resistant to lysozyme and
penicillin attack. The gram-negative outer membrane which contains LPS, an
endotoxin, blocks antibiotics, dyes, and detergents protecting the sensitive inner
membrane and cell wall.
LPS is significant in membrane transport of gram-negative bacteria. LPS, which
includes O-antigen, a core polysaccharide and a Lipid A, coats the cell surface and
works to exclude large hydrophobic compounds such as bile salts and antibiotics from
invading the cell. O-antigen are long hydrophilic carbohydrate chains (up to 50 sugars
long) that extend out from the outer membrane while Lipid A (and fatty acids)
anchors the LPS to the
Virulence-related outer membrane proteins
Virulence-related outer membrane proteins are expressed in Gram-negative bacteria
and are essential to bacterial survival within macrophages and for eukaryotic cell
invasion.
This family consists of several bacterial and phage Ail/Lom-like proteins. The
Yersinia enterocolitica Ail protein is a known virulence factor. Proteins in this family
are predicted to consist of eight transmembrane beta-sheets and four cell surfaceexposed loops. It is thought that Ail directly promotes invasion and loop 2 contains an
active site, perhaps a receptor-binding domain. The phage protein Lom is expressed
during lysogeny, and encode host-cell envelope proteins. Lom is found in the bacterial
outer membrane, and is homologous to virulence proteins of two other enterobacterial
genera. It has been suggested that lysogeny may generally have a role in bacterial
survival in animal hosts, and perhaps in pathogenesis.
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Members of this group include:
PagC, required by Salmonella typhimurium for survival in macrophages and for
virulence in mice Rck outer membrane protein of the S. typhimurium virulence
plasmid Ail, a product of the Yersinia enterocolitica chromosome capable of
mediating bacterial adherence to and invasion of epithelial cell lines
OmpX from
Escherichia coli that promotes adhesion to and entry into mammalian cells. It also has
a role in the resistance against attack by the human complement system a
Bacteriophage lambda outer membrane protein, Lom
The crystal structure of OmpX from E. coli reveals that OmpX consists of an eightstranded antiparallel all-next-neighbour beta barrel. The structure shows two girdles
of aromatic amino acid residues and a ribbon of nonpolar residues that attach to the
membrane interior. The core of the barrel consists of an extended hydrogen-bonding
network of highly conserved residues. OmpX thus resembles an inverse micelle. The
OmpX structure shows that the membrane-spanning part of the protein is much better
conserved than the extracellular loops. Moreover, these loops form a protruding beta
sheet, the edge of which presumably binds to external proteins. It is suggested that
this type of binding promotes cell adhesion and invasion and helps defend against the
complement system. Although OmpX has the same beta-sheet topology as the
structurally related outer membrane protein A (OmpA) IPR000498, their barrels differ
with respect to the shear numbers and internal hydrogen-bonding networks.
The structure of Bacterial Outer Membrane Proteins
Integral membrane proteins come in two types, a -helical and h -barrel proteins. In
both types, all hydrogen bonding donors and acceptors of the polypeptide backbone
are completely compensated and buried while nonpolar side chains point to the
membrane. The a-helical type is more abundant and occurs in cytoplasmic (or inner)
membranes, whereas the h -barrels are known from outer membranes of bacteria. The
h -barrel construction is described by the number of strands and the shear number,
which is a measure for the inclination angle of the h –strands against the barrel axis.
The common right-handed h-twist requires shear numbers slightly larger than the
number of strands. Membrane protein h -barrels contain between 8 and 22 h-strands
and have a simple topology that is probably enforced by the folding process. The
smallest barrels form inverse micelles and work as enzymes or they bind to other
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macromolecules. The medium-range barrels form more or less specific pores for
nutrient uptake, whereas the largest barrels occur in active Fe 2+ transporters. The h barrels are suitable objects forchannel engineering, because the structures are simple
and because many of these proteins can be produced into inclusion bodies and
recovered there from in the exact native conformation.
Functions of outer membrane proteins
After discussing the structures, it seems appropiate to refer also to the functions.
OmpX is synthesize d in large amounts in stress situations and it is probably used as a
defensive weapon bi nding to and thus interfering with foreign proteins. Hal f of the
OmpX h -barrel protrudes into the external medium, presenting an inclined h -sheet
edge that binds to any foreign protein with a h -strand in its surface layer. Such
proteins are ubiquitous, an example being the large group of proteins with central
parallel h -sheets surronded by a-helices. In the X-ray analysis, all loop residues of
OmpX were located in electron density indicating that the h -sheet edge presented to
the foreign proteins is rigid, as it is required for t ig ht binding. In contr ast to OmpX ,
the long external loops of Om pA are h ig hl y mo bile an d f or t he m o st p ar t no t
vi si bl e in t he respec tive elect ron d ensity map. In vivo, the mobile loops are rather
resistant to proteolytic attack, presumably because they bind to the surroun ing
lipopolysa c char ides. Obviously, the mobile loops fulfill essential functions in
bacterial life
The outer mem brane enzyme OmpT is a special protease that has been implicated in
the pathogenicty of bacteria. It is monomeric with the active center pointing to the
outside. A fu rt he r enzym e, the ph os ph ol i pa se A O m pLA, produce s holes in
the outer membrane when it is activated. The activation process has not yet been
clarified, but it is know n to require a dimerization of OmpLA in the mem -brane.
2.6 Bacterial Adhesions
Adhesins are cell-surface components or appendages of bacteria that facilitate
bacterial adhesion or adherence to other cells or to inanimate surfaces. Adhesins are a
type of virulence factor. Adherence is an essential step in bacterial pathogenesis or
infection, required for colonizing a new host. For example, nontypeable Haemophilus
influenzae expresses the adhesins Hia, Hap, Oap and a hemagglutinating pili.
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Most fimbriae of gram-negative bacteria function as adhesins, but in many cases it is
a minor subunit protein at the tip of the fimbriae that is the actual adhesin. In grampositive bacteria, a protein or polysaccharide surface layer serves as the specific
adhesin. To effectively achieve adherence to host surfaces, many bacteria produce
multiple adherence factors called adhesins.
Among the earliest events in many bacterial infections are the molecular interactions
that occur between the pathogen and host cells. These interactions are typically
required for extracellular colonization or internalization to occur and may involve a
complex cascade of molecular cross talk at the host-pathogen interface. Colonization
of host tissues is usually me-diated by adhesins on the surface of the microbe; the
adhesins are responsible for recognizing and binding to specific receptor moieties of
host cells. The receptor binding event may activate complex signal transduction
cascades in the host cell that can have diverse consequences including the activation
of innate host defenses or the subversion of cellular processes facilitat-ing bacterial
colonization or invasion. In addition, the binding event may also activate the
expression of new genes in the microbe that are important in the pathogenic process.
In many instances, adhesins are assembled into hair-like appendages called pili or
fimbriae that extend out from the bacterial sur-face. In other cases, the adhesins are
directly associated with the microbial cell surface (so-called nonpilus adhesins). Collectively, these adhesins and related structures are expressed in organisms associated
with a broad range of diseases At least four distinct mechanisms have emerged in
recent years to account for the assembly of these diverse organelles: (i) the chaperoneusher pathway, (ii) the general secretion pathway, (iii) the extracellular nucleationprecipitation pathway, and
(iv) the alternate chaperone pathway. This list is by no means all-inclusive but rather
represents some of the best-character-ized systems to date (for a recent review of
other systems that do not utilize these pathways, Molecular blueprints of these
pathways will ultimately facilitate the un-derstanding of host-pathogen interactions as
well as provide a framework for understanding how complex hetero-oligomeric
interactions are orchestrated within the bacterial cell. In this minireview, we focus on
the molecular architecture of the adhesive organelles assembled by these four
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principal path-ways and on the coordinated functions of the proteins that constitute
their assembly machineries.
MOLECULAR STRUCTURES OF FIMBRIAL ADHESINS
We begin by looking at the architectural features of various fimbrial organelles
assembled by each of the four general as-sembly pathways. We focus on the bestcharacterized systems in each pathway as prototypes for each assembly classification:
P and type 1 pili (chaperone-usher pathway), type IV pili (general secretion pathway),
curli (extracellular nucleation-precipitation pathway) and CS1 pili (alternate
chaperone path-way). Note that for the purposes of this minireview, the termsubunit
will apply to the structural proteins that make up these composite organelles, while
the term adhesin will be reserved for those subunits with specific receptor binding
properties. P pili and type 1 pili.P pili are expressed on the surfaces of uropathogenic
strains of Escherichia coli associated with acute pyelonephritis (63). Eleven genes
organized in the pap gene
cluster are required for the expression and assembly of these organelles (46, 49, 50,
78). Studies of P pili using quick-freeze, deep-etch electron microscopy have shown
that P pili are com-posite fibers consisting of flexible fibrillae joined end to end to
pilus rods (67). The tip fibrillae are comprised predominantly of PapE subunits. The
rod is composed of repeating PapA subunits packed into a right-handed helical
assembly, with an external diameter of 68 Å, an axial hole of 15 Å, and a pitch
distance of 24.9 Å, with 3.28 subunits per turn of the helical cylinder (14, 37). The
adhesin of P pili, PapG, mediates bind-ing to Gal a(1,4)Gal moieties present in the
globoseries of glycolipids on uroepithelial cells and erythrocytes (71, 111). The
adhesin is located at the distal end of the tip and is joined
to the PapE fibrillum via a specialized adapter protein, PapF. Another adapter protein,
PapK, joins the adhesin-containing tip to the PapA rod. Another minor component,
PapH, is located at the base of the PapA rod; its incorporation into the growing
organelle is thought to signal the termination of as-sembly.
Type 1 pili are important virulence determinants expressed in E. coli as well as in
most members of the Enterobacteriaceae family that mediate binding to mannoseoligosaccharides (66).The expression and assembly of type 1 pili typically require at
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least nine genes that are present in the type 1 gene cluster (46, 50). Like P pili, type 1
pili are also composite structures in which a short tip fibrillar structure containing
FimG and the FimH adhesin (and possibly the minor component FimF as well) are
joined to a rod comprised predominantly of FimA subunits (58). The overall structure
of the type 1 rod is very
similar to that of the PapA rod of P pili. The type 1 subunits are arranged in a helix
with an external diameter of 6 to 7 nmand an axial hole of 20 to 25 Å, with a pitch
distance of 23.1 Å and 3.125 subunits per turn (13). Type IV pili. Type IV pili have
been implicated in a variety of functions, including adhesion to host cell surfaces,
twitching motility, modulation of target cell specificity, and bacterio-phage
adsorption. They are found on such bacteria asPseudo-monas aeruginosa, pathogenic
Neisseria, Moraxella bovis, Dich-elobacter nodosus, Vibrio cholerae, and
enteropathogenic E. coli (EPEC) (113). The role of type IV pili in the virulence
ofEPEC strains has recently been demonstrated by Bieber and colleagues (12). These
structures have a diameter of 60 Å and are typically up to 4,000 nm long, with a pitch
distance of approximately 40 Å and about five subunits per turn (89). They are
composed predominantly of identical pilin subunits with a number of distinctive
features, including a short (6 to 7 amino acids), positively charged leader sequence, a
modified amino acid ( N-methylphenylalanine) at the amino terminus of the mature
pilin, and a highly conserved amino-terminal domain (4, 43, 91, 92). A few other
proteins also associate with these structures, including in the case of Neisseria, the tiplocalized adhesin (100). The crystal structure of a type IV pilin subunit (PilE) from
Neisseria gonorrhoeaehas recently been determined by Parge and coworkers at an
atomic resolution of 2.6 Å (89). It reveals ana-b roll fold with a rather long
hydrophobic N-terminal a 1 -helical spine (residues 2 to 54) that gives the molecule
an overall ladle shape
Curli. Many clinicalE. coli and Salmonella enteritidis isolates produce a class of thin,
irregular, and highly aggregated surface structures known as curli (17, 94). These
organelles mediate binding to a variety of host proteins, including fibronectin
(94),plasminogen (106), and human contact phase proteins (10). Curli are highly
stable structures that require extreme chemical treatment (e.g., 90% formic acid) to
depolymerize them. The major component of E. coli curli is a 15.3-kDa protein
termed CsgA, which exhibits more than 86% primary sequence simi-larity to its
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counterpart in S. enteritidis, AgfA. CsgB is a minor component that may be found
associated with the outer mem-brane (OM) or distributed along the length of the curli
fiber (11). CsgE, CsgF, and CsgG are required assembly factors that do not appear to
constitute part of the final curli structure and hence may serve as part of the assembly
apparatus (40).
CS1 pili. CS1 pili are found on the surface of EPEC and are thought to be involved in
the colonization of the host intestine (102). Other pilus structures in this family
include CS2 (30), CS4 (115), CS14 (81), CS17 (82), CS19 (38), CFA/I (61), and the
cable type II pili of the cystic fibrosis-associated pathogen Burkholderia cepacia
(101). CS1 pili appear to be composed predominantly of one component, CooA, with
a distally lo-cated minor component, CooD. Electron microscopic exami-nation of
these structures reveals that they are morphologically similar to P and type 1 pili,
although the structural proteins of CS1-like pili bear no significant sequence
similarity to those of other pilus systems (102)
2.7 Comparative Genomics applications with
significance to non-
proteobacterial species
In present research work focused on infectious disease of Non-proteobacteria because
it causes infection or disease in many countries or worldwide distribution. We
targeted on pathogenesis, bacterial strain, mode of transmission of above discussed
bacterial disease by using comparative genomics. In which gene, genome or protein
are studied and research on these disease for drug discovery for prevention of this
disease. There is no vaccines available against infections caused by nonproteobacteria
like Borrelia , Treponema species.
Comparative analysis of the genomes provide a huge and unprecedented resource for
discovering novel molecular characteristics that are either unique to particular species
or are shared by different nonproteobacteria and they can also provide valuable tools
for biochemical, diagnostic, taxonomic and evolutionary studies. It is also important
in Drug discovery. A number of comparative genomic studies have been conducted to
identify proteins,genes that are unique to particular nonproteobacterial species that
could be responsible for disease causation or virulence. Comparative genomics a
powerful approach for achieving a better understanding of the genomes and,
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subsequently, of the biology of the respective organisms. Here, we use databases that
store genomic information and bioinformatics tools that are used in the computational
analysis of complete genomes.
Computational approaches to genome comparison have recently used in biological
research and strengthened the scope of studies, ranging from whole genome
comparisons to gene expression analysis. This has increased the introduction of
different ideas, including concepts from systems and control, information theory,
strings analysis and data mining. Comparative genomics is the study of the
relationship of genome structure and function across different biological species or
strains. Comparative genomics is an attempt to take advantage of the information
provided by the signatures of selection to understand the function and evolutionary
processes that act on genomes .
Comparative genomics also exploits both similarities and differences in the proteins,
RNA, and regulatory regions of different organisms to infer how selection has acted
upon these elements. Those elements that are responsible for similarities between
different species should be conserved through time (stabilizing selection), while those
elements responsible for differences among species should be divergent (positive
selection). Finally, those elements that are unimportant to the evolutionary success of
the organism will be unconserved (selection is neutral)
Both comparative genomic/bioinformatics studies of genome data and functional
genomic studies are still in their infancy, and have yet to reach their full potential, still
are leading to the
novel findings. Comparative genomic analyses of membrane
transport systems conducted by
Ian T. Paulsen and et al have revealed that
transporter substrate specificities correlate with an organism‘s lifestyle. The types and
numbers of predicted drug efflux systems vary dramatically amongst sequenced
organisms.
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