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Article ; Online: Assessing Protein Interactions for Clustering of Mitochondrial Urea Cycle Enzymes.

Caldovic, Ljubica / Bhuvanendran, Shivaprasad / Jaiswal, Jyoti

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2487, Page(s) 73–92

Abstract: Enzyme clustering is a phenomenon that involves partitioning of proteins that function together in a common subcellular or sub-organellar compartment. Traditional genetic, biochemical, and biophysical approaches for studying protein-protein interactions ... ...

Abstract	Enzyme clustering is a phenomenon that involves partitioning of proteins that function together in a common subcellular or sub-organellar compartment. Traditional genetic, biochemical, and biophysical approaches for studying protein-protein interactions in complexes with defined stoichiometry yield inconclusive results when applied to clustered proteins. This chapter describes a combination of approaches to study clustered proteins including co-immunoprecipitation, biochemical co-localization in purified mitochondria, and super resolution imaging of endogenous proteins in situ. These approaches can be used to study interactions among proteins that form clusters. We will illustrate this approach by using the urea cycle enzymes that localize in the mitochondrial matrix, and form clusters at the inner mitochondrial membrane.
MeSH term(s)	Cluster Analysis ; Mitochondria/metabolism ; Mitochondrial Membranes/metabolism ; Urea/analysis
Chemical Substances	Urea (8W8T17847W)
Language	English
Publishing date	2022-06-03
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2269-8_5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Transcription factor Ap2b regulates the mouse autosomal recessive polycystic kidney disease genes,

Wu, Maoqing / Harafuji, Naoe / O'Connor, Amber K / Caldovic, Ljubica / Guay-Woodford, Lisa M

Frontiers in molecular biosciences

2023 Volume 9, Page(s) 946344

Abstract: Transcription factor Ap2b (TFAP2B), an AP-2 family transcription factor, binds to the palindromic consensus DNA sequence, 5'- ... ...

Abstract	Transcription factor Ap2b (TFAP2B), an AP-2 family transcription factor, binds to the palindromic consensus DNA sequence, 5'-GCCN
Language	English
Publishing date	2023-01-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2022.946344
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Article ; Online: NAGS

Owusu-Ansah, Melissa / Guptan, Nikita / Alindogan, Dylon / Morizono, Michio / Caldovic, Ljubica

International journal of molecular sciences

2023 Volume 24, Issue 7

Abstract: Urea cycle enzymes and transporters collectively convert ammonia into urea in the liver. Aberrant overexpression of carbamylphosphate synthetase 1 ( ...

Abstract	Urea cycle enzymes and transporters collectively convert ammonia into urea in the liver. Aberrant overexpression of carbamylphosphate synthetase 1 (
MeSH term(s)	Humans ; Adenocarcinoma of Lung/genetics ; Amino-Acid N-Acetyltransferase/genetics ; Arginine ; Glioblastoma ; Ligases ; Mitochondrial Membrane Transport Proteins/genetics ; RNA, Messenger ; Urea/metabolism ; Carbamoyl-Phosphate Synthase (Ammonia)/genetics
Chemical Substances	Amino-Acid N-Acetyltransferase (EC 2.3.1.1) ; Arginine (94ZLA3W45F) ; citrin (1340-08-5) ; Ligases (EC 6.-) ; Mitochondrial Membrane Transport Proteins ; RNA, Messenger ; SLC25A13 protein, human ; Urea (8W8T17847W) ; NAGS protein, human (EC 2.3.1.1) ; CPS1 protein, human (EC 6.3.4.16) ; Carbamoyl-Phosphate Synthase (Ammonia) (EC 6.3.4.16)
Language	English
Publishing date	2023-04-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24076754
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Article ; Online: Transcription factor Ap2b regulates the mouse autosomal recessive polycystic kidney disease genes, Pkhd1 and Cys1

Maoqing Wu / Naoe Harafuji / Amber K. O’Connor / Ljubica Caldovic / Lisa M. Guay-Woodford

Frontiers in Molecular Biosciences, Vol

2023 Volume 9

Abstract: Transcription factor Ap2b (TFAP2B), an AP-2 family transcription factor, binds to the palindromic consensus DNA sequence, 5′-GCCN3-5GGC-3’. Mice lacking functional Tfap2b gene die in the perinatal or neonatal period with cystic dilatation of the kidney ... ...

Abstract	Transcription factor Ap2b (TFAP2B), an AP-2 family transcription factor, binds to the palindromic consensus DNA sequence, 5′-GCCN3-5GGC-3’. Mice lacking functional Tfap2b gene die in the perinatal or neonatal period with cystic dilatation of the kidney distal tubules and collecting ducts, a phenotype resembling autosomal recessive polycystic kidney disease (ARPKD). Human ARPKD is caused by mutations in PKHD1, DZIP1L, and CYS1, which are conserved in mammals. In this study, we examined the potential role of TFAP2B as a common regulator of Pkhd1 and Cys1. We determined the transcription start site (TSS) of Cys1 using 5′ Rapid Amplification of cDNA Ends (5′RACE); the TSS of Pkhd1 has been previously established. Bioinformatic approaches identified cis-regulatory elements, including two TFAP2B consensus binding sites, in the upstream regulatory regions of both Pkhd1 and Cys1. Based on reporter gene assays performed in mouse renal collecting duct cells (mIMCD-3), TFAP2B activated the Pkhd1 and Cys1 promoters and electromobility shift assay (EMSA) confirmed TFAP2B binding to the in silico identified sites. These results suggest that Tfap2b participates in a renal epithelial cell gene regulatory network that includes Pkhd1 and Cys1. Disruption of this network impairs renal tubular differentiation, causing ductal dilatation that is the hallmark of recessive PKD.
Keywords	autosomal recessive polycystic kidney disease (ARPKD) ; Cys1 ; Pkhd1 ; Tfap2b ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: NAGS , CPS1 , and SLC25A13 (Citrin) at the Crossroads of Arginine and Pyrimidines Metabolism in Tumor Cells

Melissa Owusu-Ansah / Nikita Guptan / Dylon Alindogan / Michio Morizono / Ljubica Caldovic

International Journal of Molecular Sciences, Vol 24, Iss 6754, p

2023 Volume 6754

Abstract: Urea cycle enzymes and transporters collectively convert ammonia into urea in the liver. Aberrant overexpression of carbamylphosphate synthetase 1 ( CPS1 ) and SLC25A13 (citrin) genes has been associated with faster proliferation of tumor cells due to ... ...

Abstract	Urea cycle enzymes and transporters collectively convert ammonia into urea in the liver. Aberrant overexpression of carbamylphosphate synthetase 1 ( CPS1 ) and SLC25A13 (citrin) genes has been associated with faster proliferation of tumor cells due to metabolic reprogramming that increases the activity of the CAD complex and pyrimidine biosynthesis. N-acetylglutamate (NAG), produced by NAG synthase (NAGS), is an essential activator of CPS1. Although NAGS is expressed in lung cancer derived cell lines, expression of the NAGS gene and its product was not evaluated in tumors with aberrant expression of CPS1 and citrin. We used data mining approaches to identify tumor types that exhibit aberrant overexpression of NAGS , CPS1 , and citrin genes, and evaluated factors that may contribute to increased expression of the three genes and their products in tumors. Median expression of NAGS , CPS1 , and citrin mRNA was higher in glioblastoma multiforme (GBM), glioma, and stomach adenocarcinoma (STAD) samples compared to the matched normal tissue. Median expression of CPS1 and citrin mRNA was higher in the lung adenocarcinoma (LUAD) sample while expression of NAGS mRNA did not differ. High NAGS expression was associated with an unfavorable outcome in patients with glioblastoma and GBM. Low NAGS expression was associated with an unfavorable outcome in patients with LUAD. Patterns of DNase hypersensitive sites and histone modifications in the upstream regulatory regions of NAGS , CPS1 , and citrin genes were similar in liver tissue, lung tissue, and A549 lung adenocarcinoma cells despite different expression levels of the three genes in the liver and lung. Citrin gene copy numbers correlated with its mRNA expression in glioblastoma, GBM, LUAD, and STAD samples. There was little overlap between NAGS , CPS1, and citrin sequence variants found in patients with respective deficiencies, tumor samples, and individuals without known rare genetic diseases. The correlation between NAGS , CPS1 , and citrin mRNA expression in the ...
Keywords	N-acetylglutamate synthase ; carbamylphosphate synthetase 1 ; citrin ; urea cycle ; pyrimidine biosynthesis ; CAD complex ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	570
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Fifteen years of urea cycle disorders brain research: Looking back, looking forward

Sen, Kuntal / Whitehead, Matthew / Castillo Pinto, Carlos / Caldovic, Ljubica / Gropman, Andrea

Analytical biochemistry. 2022 Jan. 01, v. 636

2022

Abstract: Urea cycle disorders (UCD) are inherited diseases resulting from deficiency in one of six enzymes or two carriers that are required to remove ammonia from the body. UCD may be associated with neurological damage encompassing a spectrum from asymptomatic/ ... ...

Abstract	Urea cycle disorders (UCD) are inherited diseases resulting from deficiency in one of six enzymes or two carriers that are required to remove ammonia from the body. UCD may be associated with neurological damage encompassing a spectrum from asymptomatic/mild to severe encephalopathy, which results in most cases from Hyperammonemia (HA) and elevation of other neurotoxic intermediates of metabolism. Electroencephalography (EEG), Magnetic resonance imaging (MRI) and Proton Magnetic resonance spectroscopy (MRS) are noninvasive measures of brain function and structure that can be used during HA to guide management and provide prognostic information, in addition to being research tools to understand the pathophysiology of UCD associated brain injury. The Urea Cycle Rare disorders Consortium (UCDC) has been invested in research to understand the immediate and downstream effects of hyperammonemia (HA) on brain using electroencephalogram (EEG) and multimodal brain MRI to establish early patterns of brain injury and to track recovery and prognosis. This review highlights the evolving knowledge about the impact of UCD and HA in particular on neurological injury and recovery and use of EEG and MRI to study and evaluate prognostic factors for risk and recovery. It recognizes the work of others and discusses the UCDC's prior work and future research priorities.
Keywords	ammonia ; brain ; brain damage ; electroencephalography ; encephalopathy ; magnetism ; metabolism ; neurotoxicity ; nuclear magnetic resonance spectroscopy ; pathophysiology ; prognosis ; risk ; urea cycle
Language	English
Dates of publication	2022-0101
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2021.114343
Database	NAL-Catalogue (AGRICOLA)

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Article: Differential regulation of MYC expression by

Harafuji, Naoe / Yang, Chaozhe / Wu, Maoqing / Thiruvengadam, Girija / Gordish-Dressman, Heather / Thompson, R Griffin / Bell, P Darwin / Rosenberg, Avi Z / Dafinger, Claudia / Liebau, Max C / Bebok, Zsuzsanna / Caldovic, Ljubica / Guay-Woodford, Lisa M

Frontiers in cell and developmental biology

2023 Volume 11, Page(s) 1270980

Abstract: Autosomal recessive polycystic kidney disease (ARPKD; MIM#263200) is a severe, hereditary, hepato-renal fibrocystic disorder that leads to early childhood morbidity and mortality. Typical forms of ARPKD are caused by pathogenic variants in ... ...

Abstract	Autosomal recessive polycystic kidney disease (ARPKD; MIM#263200) is a severe, hereditary, hepato-renal fibrocystic disorder that leads to early childhood morbidity and mortality. Typical forms of ARPKD are caused by pathogenic variants in the
Language	English
Publishing date	2023-11-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2023.1270980
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Article ; Online: Fifteen years of urea cycle disorders brain research: Looking back, looking forward.

Sen, Kuntal / Whitehead, Matthew / Castillo Pinto, Carlos / Caldovic, Ljubica / Gropman, Andrea

Analytical biochemistry

2021 Volume 636, Page(s) 114343

Abstract	Urea cycle disorders (UCD) are inherited diseases resulting from deficiency in one of six enzymes or two carriers that are required to remove ammonia from the body. UCD may be associated with neurological damage encompassing a spectrum from asymptomatic/mild to severe encephalopathy, which results in most cases from Hyperammonemia (HA) and elevation of other neurotoxic intermediates of metabolism. Electroencephalography (EEG), Magnetic resonance imaging (MRI) and Proton Magnetic resonance spectroscopy (MRS) are noninvasive measures of brain function and structure that can be used during HA to guide management and provide prognostic information, in addition to being research tools to understand the pathophysiology of UCD associated brain injury. The Urea Cycle Rare disorders Consortium (UCDC) has been invested in research to understand the immediate and downstream effects of hyperammonemia (HA) on brain using electroencephalogram (EEG) and multimodal brain MRI to establish early patterns of brain injury and to track recovery and prognosis. This review highlights the evolving knowledge about the impact of UCD and HA in particular on neurological injury and recovery and use of EEG and MRI to study and evaluate prognostic factors for risk and recovery. It recognizes the work of others and discusses the UCDC's prior work and future research priorities.
MeSH term(s)	Animals ; Brain/diagnostic imaging ; Brain/metabolism ; Brain/physiopathology ; Electroencephalography ; History, 21st Century ; Hyperammonemia/diagnostic imaging ; Hyperammonemia/history ; Hyperammonemia/metabolism ; Hyperammonemia/physiopathology ; Magnetic Resonance Imaging ; Proton Magnetic Resonance Spectroscopy ; Urea Cycle Disorders, Inborn/diagnostic imaging ; Urea Cycle Disorders, Inborn/history ; Urea Cycle Disorders, Inborn/metabolism ; Urea Cycle Disorders, Inborn/physiopathology
Language	English
Publishing date	2021-10-09
Publishing country	United States
Document type	Historical Article ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2021.114343
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Article: Sources and Fates of Carbamyl Phosphate: A Labile Energy-Rich Molecule with Multiple Facets.

Shi, Dashuang / Caldovic, Ljubica / Tuchman, Mendel

Biology

2018 Volume 7, Issue 2

Abstract: Carbamyl phosphate (CP) is well-known as an essential intermediate of pyrimidine and arginine/urea biosynthesis. Chemically, CP can be easily synthesized from dihydrogen phosphate and cyanate. Enzymatically, CP can be synthesized using three different ... ...

Abstract	Carbamyl phosphate (CP) is well-known as an essential intermediate of pyrimidine and arginine/urea biosynthesis. Chemically, CP can be easily synthesized from dihydrogen phosphate and cyanate. Enzymatically, CP can be synthesized using three different classes of enzymes: (1) ATP-grasp fold protein based carbamyl phosphate synthetase (CPS); (2) Amino-acid kinase fold carbamate kinase (CK)-like CPS (anabolic CK or aCK); and (3) Catabolic transcarbamylase. The first class of CPS can be further divided into three different types of CPS as CPS I, CPS II, and CPS III depending on the usage of ammonium or glutamine as its nitrogen source, and whether
Language	English
Publishing date	2018-06-12
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology7020034
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Article ; Online: Pkhd1

Yang, Chaozhe / Harafuji, Naoe / Caldovic, Ljubica / Yu, Weiying / Boddu, Ravindra / Bhattacharya, Surajit / Barseghyan, Hayk / Gordish-Dressman, Heather / Foreman, Oded / Bebok, Zsuzsa / Eicher, Eva M / Guay-Woodford, Lisa M

Journal of molecular medicine (Berlin, Germany)

2023 Volume 101, Issue 9, Page(s) 1141–1151

Abstract: Autosomal-recessive polycystic kidney disease (ARPKD; MIM #263200) is a severe, hereditary, hepato-renal fibrocystic disorder that causes early childhood morbidity and mortality. Mutations in the polycystic kidney and hepatic disease 1 (PKHD1) gene, ... ...

Abstract	Autosomal-recessive polycystic kidney disease (ARPKD; MIM #263200) is a severe, hereditary, hepato-renal fibrocystic disorder that causes early childhood morbidity and mortality. Mutations in the polycystic kidney and hepatic disease 1 (PKHD1) gene, which encodes the protein fibrocystin/polyductin complex (FPC), cause all typical forms of ARPKD. Several mouse lines carrying diverse, genetically engineered disruptions in the orthologous Pkhd1 gene have been generated, but none expresses the classic ARPKD renal phenotype. In the current study, we characterized a spontaneous mouse Pkhd1 mutation that is transmitted as a recessive trait and causes cysticliver (cyli), similar to the hepato-biliary disease in ARPKD, but which is exacerbated by age, sex, and parity. We mapped the mutation to Chromosome 1 and determined that an insertion/deletion mutation causes a frameshift within Pkhd1 exon 48, which is predicted to result in a premature termination codon (UGA). Pkhd1
MeSH term(s)	Child, Preschool ; Mice ; Humans ; Animals ; Polycystic Kidney, Autosomal Recessive/genetics ; Polycystic Kidney, Autosomal Recessive/pathology ; Kidney/metabolism ; Mutation ; Liver Diseases ; Transcription Factors/genetics ; RNA, Messenger/genetics ; Receptors, Cell Surface/genetics
Chemical Substances	Transcription Factors ; RNA, Messenger ; Pkhd1 protein, mouse ; Receptors, Cell Surface
Language	English
Publishing date	2023-08-16
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1223802-8
ISSN	1432-1440 ; 0946-2716
ISSN (online)	1432-1440
ISSN	0946-2716
DOI	10.1007/s00109-023-02351-2
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