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Pet Cat Cit TSI Urease Ind MR VP D S L MSA Starch Nitrate

reduced

Citrobacter freundii

+ + A/A

H2S

(+) - + - A* A* A* - - +

B. subtilis + - K/A - - A K K - + +

B. megaterium + - K/A - - A K K - + -B. thuringensis + - K/A - - A K K - + +

Enterobacter 

aerogenes

+ + A/A

Gas

- - - + A/* A/* A/* - - +

E. coli + - A/A

Gas

- + + - A/* A A/* - - +

Klebsiella

pneumoniae

+ + A/A

Gas

+- - +/- A/* A/* A/* - - +

M. roseus + - A/K - - K K K + - +

M. luteus + - A/K - - K K K + - +

Proteusvulgaris

+ V K/

H2S

FeS

+ + + - A/* A K - - +

Pseudomonas

aeroginosa

+ + K/K - - - - K K K - - + (after  zinc)

Serratiamarcescens

+ + K/A

Gas

- - +/- + A +/-gas

K K - - +

Staphylococcus

aureus

+ - A/A - -   A a A +/A - +

S. epidermidis + - A/A + - A A A + - +S.saprophyticus

+ - A/A + -   A a a + - -

Salmonella

typhimurium

+ + K/A

H2S

FeS

- - + - A* K K - - +

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ATCC :- Anatomical Therapeutic Chemical Classification System.

Topoisomerase

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Topoisomerases (type I: EC 5.99.1.2, type II: EC 5.99.1.3) are enzymes that act on the topology of 

DNA, discovered by James C. Wang. [1] The double-helical configuration that DNA strands naturallyreside in makes them difficult to separate, and yet they must be separated by helicase proteins if other 

enzymes are to transcribe the sequences that encode  proteins, or if  chromosomes are to be replicated.

In so-called circular DNA, in which double helical DNA is bent around and joined in a circle, the twostrands are topologically linked, or knotted. Otherwise identical loops of DNA having different

numbers of twists are topoisomers, and cannot be interconverted by any process that does not involve

the breaking of DNA strands. Topoisomerases catalyze and guide the unknotting of DNA.

The insertion of viral DNA into chromosomes and other forms of recombination can also require theaction of topoisomerases.

Many drugs operate through interference with the topoisomerases. The broad-spectrum

fluoroquinolone antibiotics act by disrupting the function of bacterial type II topoisomerases. Some

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chemotherapy drugs work by interfering with topoisomerases in cancer  cells: type 1 is inhibited by

irinotecan and topotecan, while type 2 is inhibited by etoposide and teniposide.

Contents

[hide]

• 1 Topological problems

• 2 Type I topoisomerases

• 3 Type II topoisomerases

• 4 References

• 5 See also

[edit] Topological problems

Image:Ma05f01.jpg 

Reactions controlled by topoisomerases.There are three main types of topology; supercoiling, knotting and catenation. When outside of 

replication or transcription DNA needs to be kept as compact as possible and these three states help

this cause. However when transcription or replication occur DNA needs to be free and these statesseriously hinder the processes. Topoisomerases can fix this and are separated into two types separated

 by the number of strands cut in one round of action.

[edit] Type I topoisomerases

Both type I and type II topoisomerases change the supercoiling of DNA. Type I topoisomerasesfunction by nicking one of the strands of the DNA double helix, twisting it around the other strand,

and re-ligating the nicked strand. This is not an active process in the sense that energy in the form of 

ATP is not spent by the topoisomerase during uncoiling of the DNA; rather, the torque present in theDNA drives the uncoiling. Type I enzymes can be further subdivided into type IA and type IB, based

on their chemistry of action. Type IA topoisomerases change the linking number  of a circular DNA

strand by units of strictly 1, wherease Type IB topoisomerases change the linking number by multiples

of 1. All topoisomerases form a phosphotyrosine intermediate between the catalytic tyrosine of theenzyme and the scissile phosphoryl of the DNA backbone. Type IA topoisomerases form a covalent

linkage between the catalytic tyrosine and the 5'-phosphoryl while type IB enzymes form a covalent

3'-phosphotyrosine intermediate. Apart from these similarities, they have very different mechanisms of 

action, have different crystal structures and appear not to have similar evolutionary ancestors.

[edit] Type II topoisomerases

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Structure of the 42 KDa fragment of the N-terminal of DNA gyrase homologous to all other type IIA

topoisomerases.

Type II topoisomerases cut both strands of the DNA helix simultaneously. Once cut, the ends of theDNA are separated, and a second DNA duplex is passed through the break. Following passage, the cut

DNA is resealed. This reaction allows type II topoisomerases to increase or decrease the linking

number of a DNA loop by 2 units, and promotes chromosome disentanglement. For example, DNA

gyrase, a type II topoisomerase observed in E. coli and most other  prokaryotes, introduces negativesupercoils and decreases the linking number by 2. Gyrase also is able to remove knots from the

 bacterial chromosome. There are two subclasses of type II topoisomerases, type IIA and IIB. Type IIA

topoisomerases include the enzymes DNA gyrase, eukaryotic topoisomerase II, and bacterialtopoisomerase IV. Type IIB topoisomerases are structurally and biochemically distinct, and comprise

a single family member, topoisomerase VI. Type IIB topoisomerases are found in archaea and some

higher plants. In cancers, the topoisomerase IIalpha is highly expressed in highly proliferating cells. Incertain cancers, such as peripheral nerve sheath tumors, high expression of its encoded protein is also

associated to poor patient survival.

Catenation is where two circular DNA strands are linked together like chain links. This occurs after 

DNA replication where two single strands are catenated can still replicate but cannot separate into thetwo daughter cells. As Type II topoisomerses break a double strand they can fix this state (Type I

topoisomerases could only do this if there was a single strand nick) and the correct chromosome

number can remain in daughter cells. As linear DNA in eukaryotes is so long they can be thought of ascircular and Type II topoisomerases are needed for the same reason.

Topoisomerase IV

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Topoisomerase IV is one of two type-II topoisomerases in bacteria, the other being DNA gyrase. Like

gyrase, topoisomerase IV is able to pass one double-strand of DNA through another double-strand of 

DNA, thereby changing the linking number  of DNA by two in each enzymatic step. Topoisomerase IVhas two functions in the cell. First, it is responsible for unlinking, or decatenating, DNA following

DNA replication. The double-helical nature of  DNA and its semi-conservative mode of replication

causes the two newly replicated DNA strands to be interlinked. These links must be removed in order for the chromosome (and plasmids) to segregate into daughter cells so that cell division can complete.

Topoisomerase IV's second function in the cell is to relax positive supercoils. It shares this role with

DNA gyrase, which is also able to relax positive supercoils. Together, gyrase and topoisomerase IVremove the positive supercoils that accumulate ahead of a translocating DNA polymerase, allowing

DNA replication to continue unhindered by topological strain. Topoisomerase IV is also a target of 

antibiotics, such as the quinolone drugs, which include ciprofloxacin.

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Categories: EC 5.99.1 | Enzyme stubs