The pyrimidine biosynthesis operon of the thermophile Bacillus caldolyticus includes genes for uracil phosphoribosyltransferase and uracil permease

Ghim, Sa‐Youl; Neuhard, Jan

doi:10.1128/jb.176.12.3698-3707.1994

Cited by 53 publications

(62 citation statements)

References 51 publications

(43 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…A remarkable property of PyrR, first discovered by Ghim and Neuhard in studies of PyrR from the thermophile Bacillus caldolyticus (7), is that it also catalyzes the uracil phosphoribosyltransferase (UPRTase) 1 reaction. This finding was unexpected because the deduced amino acid sequences of PyrR proteins from various bacteria bear no significant sequence similarity outside of a short sequence in the active site to the sequences of previously characterized bacterial UPRTases, which are encoded by upp genes (1).…”

mentioning

confidence: 99%

Kinetic Studies of the Uracil Phosphoribosyltransferase Reaction Catalyzed by the Bacillus subtilis Pyrimidine Attenuation Regulatory Protein PyrR

Grabner

Switzer

2003

Journal of Biological Chemistry

View full text Add to dashboard Cite

for PyrR that include a kinetically irreversible conformational change after binding of PRPP but before uracil binding were shown to account for the Ping Pong pattern of the enzyme. This mechanism was supported by the following experimental observations. The reverse reaction was extremely slow with a catalytic rate constant 3300 times smaller than for the forward reaction. Patterns of product inhibition of the forward reaction were consistent with a version of the irreversible conformational change model in which PyrR returns to the unliganded conformation before dissociation of UMP and were inconsistent with several other kinetic mechanisms. UMP and phosphoribosylpyrophosphate were shown by equilibrium dialysis to bind to free PyrR (dissociation constants of 27 ؎ 3 and 18 ؎ 2 M, respectively), but uracil and PP i did not bind at equilibrium concentrations up to 750 M. We propose that the conformational change kinetic model developed for PyrR can also account for numerous other reports of Ping Pong kinetics for various phosphoribosyltransferases that do not form the phosphoribosyl-enzyme intermediate predicted by classic Ping Pong kinetics.

show abstract

mentioning

confidence: 99%

Kinetic Studies of the Uracil Phosphoribosyltransferase Reaction Catalyzed by the Bacillus subtilis Pyrimidine Attenuation Regulatory Protein PyrR

Grabner

Switzer

2003

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…Further examination of the conserved putative PyrR binding sequences in the three B. subtilis pyr attenuation regions, together with corresponding sequences from the B. caldolyticus pyr operon (3), revealed that each sequence is capable of folding into a stem-loop in which the most highly conserved region (UCCAGAGAGG in B. subtilis) is located at the top of the structure. The formation of such a stem-loop would in each case disrupt the base pairing between the 5Ј and the 3Ј strands of the AT stem.…”

mentioning

confidence: 99%

Function of RNA secondary structures in transcriptional attenuation of the Bacillus subtilis pyr operon

Turner

Switzer

1996

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The Bacillus subtilis pyr operon is regulated by exogenous pyrimidines by a transcriptional attenuation mechanism. Transcription in vitro from pyr DNA templates specifying attenuation regions yielded terminated and read-through transcripts of the expected lengths. Addition of the PyrR regulatory protein plus UMP led to greatly increased termination. Synthetic antisense deoxyoligonucleotides were used to probe possible secondary structures in the pyr mRNA that were proposed to play roles in controlling attenuation. Oligonucleotides predicted to disrupt terminator structures suppressed termination, whereas oligonucleotides predicted to disrupt the stem of antiterminator stem-loops strongly promoted termination at the usual termination site. Oligonucleotides that disrupt a previously unrecognized stem-loop structure, called the antiantiterminator, the formation of which interferes with formation of the downstream antiterminator, suppressed termination. We propose that transcriptional attenuation of the pyr operon is governed by switching between alternative antiterminator versus anti-antiterminator plus terminator structures, and that PyrR acts by UMP-dependent binding to and stabilization of the anti-antiterminator.Transcription of the Bacillus subtilis pyrimidine biosynthetic (pyr) operon is regulated by an attenuation mechanism that involves a regulatory protein, PyrR, which is encoded by the first gene of the operon (1, 2). PyrR is thought to act by modulating the function of three attenuators in the operon. These attenuators are located in the pyr 5Ј leader, between the first and second genes, and between the second and third genes of the operon. Each attenuation region is predicted to specify mRNA that is capable of folding into a factor-independent transcription terminator (T) stem-loop, the formation of which can be prevented by the formation of a competing and more stable upstream stem-loop, called the antiterminator (AT). The balance between read-through, with consequent expression of downstream genes, versus termination and reduced expression of pyr genes has been proposed to be determined by the interconversion between AT and T structures in the mRNA, mediated in a UMP-dependent manner by the binding of PyrR to a conserved sequence in the 5Ј strand of each AT stem. PyrR binding would destabilize the AT secondary structure and favor the formation of the alternative T secondary structure. This model was supported by the analysis of expression of pyr-lacZ fusions in which portions of the 5Ј leader specifying the proposed AT and T structures were deleted (1).Further examination of the conserved putative PyrR binding sequences in the three B. subtilis pyr attenuation regions, together with corresponding sequences from the B. caldolyticus pyr operon (3), revealed that each sequence is capable of folding into a stem-loop in which the most highly conserved region (UCCAGAGAGG in B. subtilis) is located at the top of the structure. The formation of such a stem-loop would in each case disrupt the base pair...

show abstract

“…These promoters are PyrB for the carbamoyl phosphate small chain (carA or pyrAA) and PyrC for the carbamoyl phosphate large chain (carB). In all organisms, there are two ways of synthesizing the pyrimidine nucleotides, either using the salvage pathways of preformed nucleosides and pyrimidine bases or from bicarbonate and intermediaries of the central metabolism using the de novo pathway (Ghim and Neuhard) [21]. The de novo pathway is catalysed by ATP, glutamine (ammonia), aspartate and 5-phosphoribosyl-1-pyrophosphate (PRPP) and by bicarbonate and UMP when the exogenous pyrimidines are not present in the culture.…”

Section: Discussionmentioning

confidence: 99%

“…This process is performed using six different enzymes that are encoded by the pyr operon: aspartate transcarbamoylase (pyrB), dihydroorotase (pyrC), dihydroorotate dehydrogenase (pyrD), carbamoylphosphate synthetase (carAB in enteric bacteria and pyrA in Bacillus spp. ), orotate phosphoribosyltransferase (pyrE) and orotidine 5'-phosphate decarboxylase (pyrF) [21].…”

Section: Discussionmentioning

confidence: 99%

Using Different Bioinformatics Software Tools for Determining the Carbon Dioxide (CO2) Dependence in Staphhylococcus aureus

Sa¹,

Alsuhibany²

2015

J Comput Sci Syst Biol

View full text Add to dashboard Cite

Keywords: Staphylococcus aureus; CO 2 -dependent S. aureus strains;MUMmer; BLAST; Jalview; ClustalW IntroductionStaphylococcus aureus (S. aureus) is a Gram-positive, immobile and spherically shaped (around 1 μm diameter) bacterium that occurs in microscopic bunches similar to grapes, as shown in Figure 1. In general, S. aureus shows two different colonies; on agar dishes S. aureus forms huge golden yellow colonies, while on blood agar dishes it has haemolytic properties. In addition, S. aureus has the ability to produce the lactic acid as it is considered to be an optional anaerobic, which grows either by aerobic respiration or by fermentation [2].Commonly, S. aureus can be found on the skin, like part of the regular flora and in the respiratory tract of the human. Furthermore, this bacterium can be found as skin lesions or impetigo in the adult individual as an abscess in children or as mastitis in cattle [3,4]. It has been recorded that, around 20% of the populations are considered to have a long-term case of S. aureus. Moreover, there are different diseases that can be caused by S. aureus such as soft tissue infections, life-threatening septicaemia, superficial skin, endocarditis and toxic shock syndrome [5]. In most cases β-lactam antibiotics, clindamycin, tetracycline and sulpha drugs are using as treatments for the S. aureus infections. In the past, before introducing penicillin as a treatment in 1949, the major cause of mortality in patients was the hospital-acquired (nosocomial) infections, which are caused by S. aureus. After that, the penicillin-resistant S. aureus isolates were first discovered in hospitals. Then the first discovery of the Methicillin-resistant nosocomial S. aureus isolates was in 1961 [6]. Afterwards, in hospitals and intensive care units the Methicillin-resistant S. aureus (MRSA) became common worldwide. Nowadays, more than 30% of the bacterial nosocomial infections occurring in intensive care units are caused by MRSA. Previously, MRSA was confined only to hospitals and then new strains of MRSA arose in the community causing different infections in healthy humans. In the 1990s, an extreme Community-Acquired Methicillinresistant S. aureus (CA-MRSA) strain was discovered in Australia [7]. Normally, CA-MRSA has the ability to cause different infections such as a spontaneous abscess either on the skin or on the soft-tissues. In addition, the CA-MRSA strains can be spread quickly in a community, and can affect children and healthy individuals.Pinto and Merlino found that the CO2-dependent S. aureus was detected for the first time in 1955 [8]. These organisms can be found as an inhabitant of small colony variant (SCV) S. aureus, which can cause recurrent and persistent infections. In addition, SCV S. aureus AbstractStaphylococcus aureus (S. aureus) is a Gram-positive bacterium that occurs in microscopic bunches similar to grapes. In general, S. aureus shows two different colonies; on agar dishes S. aureus forms huge golden yellow colonies, while on blood agar dishes it has haemolytic prop...

show abstract

The pyrimidine biosynthesis operon of the thermophile Bacillus caldolyticus includes genes for uracil phosphoribosyltransferase and uracil permease

Cited by 53 publications

References 51 publications

Kinetic Studies of the Uracil Phosphoribosyltransferase Reaction Catalyzed by the Bacillus subtilis Pyrimidine Attenuation Regulatory Protein PyrR

Kinetic Studies of the Uracil Phosphoribosyltransferase Reaction Catalyzed by the Bacillus subtilis Pyrimidine Attenuation Regulatory Protein PyrR

Function of RNA secondary structures in transcriptional attenuation of the Bacillus subtilis pyr operon

Using Different Bioinformatics Software Tools for Determining the Carbon Dioxide (CO2) Dependence in Staphhylococcus aureus

Contact Info

Product

Resources

About