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Article ; Online: Plasmodium falciparum

Shrivastava, Deepti / Jha, Akanksha / Kabrambam, Rajlakshmi / Vishwakarma, Jyoti / Mitra, Kalyan / Ramachandran, Ravishankar / Habib, Saman

ACS infectious diseases

2024 Volume 10, Issue 1, Page(s) 155–169

Abstract: Replication of the malarial parasite in human erythrocytes requires massive zinc fluxes, necessitating the action of zinc transporters across the parasite plasma and organellar membranes. Although genetic knockout studies have been conducted on a few " ... ...

Abstract	Replication of the malarial parasite in human erythrocytes requires massive zinc fluxes, necessitating the action of zinc transporters across the parasite plasma and organellar membranes. Although genetic knockout studies have been conducted on a few "orphan" zinc transporters in
MeSH term(s)	Animals ; Humans ; Plasmodium falciparum/metabolism ; Apicoplasts/metabolism ; Parasites ; Cell Membrane ; Erythrocytes/parasitology
Language	English
Publishing date	2024-01-01
Publishing country	United States
Document type	Journal Article
ISSN	2373-8227
ISSN (online)	2373-8227
DOI	10.1021/acsinfecdis.3c00426
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Article ; Online: [Fe-S] biogenesis and unusual assembly of the ISC scaffold complex in the Plasmodium falciparum mitochondrion.

Mohammad Sadik / Mohammad Afsar / Ramachandran, Ravishankar / Habib, Saman

Molecular microbiology

2021 Volume 116, Issue 2, Page(s) 606–623

Abstract: The malaria parasite harbors two [Fe-S] biogenesis pathways of prokaryotic origin-the SUF and ISC systems in the apicoplast and mitochondrion, respectively. While the SUF machinery has been delineated, there is little experimental evidence on the ISC ... ...

Abstract	The malaria parasite harbors two [Fe-S] biogenesis pathways of prokaryotic origin-the SUF and ISC systems in the apicoplast and mitochondrion, respectively. While the SUF machinery has been delineated, there is little experimental evidence on the ISC pathway. We confirmed mitochondrial targeting of Plasmodium falciparum ISC proteins followed by analyses of cysteine desulfurase, scaffold, and [Fe-S]-carrier components. PfIscU functioned as the scaffold in complex with the PfIscS-PfIsd11 cysteine desulfurase and could directly assemble [4Fe-4S] without prior [2Fe-2S] formation seen in other homologs. Small angle X-ray scattering and spectral studies showed that PfIscU, a trimer, bound one [4Fe-4S]. In a deviation from reported complexes from other organisms, the P. falciparum desulfurase-scaffold complex assembled around a PfIscS tetramer instead of a dimer, resulting in a symmetric hetero-hexamer [2× (2PfIscS-2PfIsd11-2PfIscU)]. PfIscU directly transferred [4Fe-4S] to the apo-protein aconitase B thus abrogating the requirement of intermediary proteins for conversion of [2Fe-2S] to [4Fe-4S] before transfer to [4Fe-4S]-recipients. Among the putative cluster-carriers, PfIscA2 was more efficient than PfNifU-like protein; PfIscA1 primarily bound iron, suggesting its potential role as a Fe
MeSH term(s)	Aconitate Hydratase/metabolism ; Carbon-Sulfur Lyases/metabolism ; Carrier Proteins/metabolism ; Humans ; Iron-Sulfur Proteins/biosynthesis ; Malaria, Falciparum/pathology ; Mitochondria/metabolism ; Plasmodium falciparum/metabolism ; Protein Multimerization
Chemical Substances	Carrier Proteins ; Iron-Sulfur Proteins ; Aconitate Hydratase (EC 4.2.1.3) ; Carbon-Sulfur Lyases (EC 4.4.-) ; cysteine desulfurase (EC 4.4.1.-)
Language	English
Publishing date	2021-06-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/mmi.14735
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Article ; Online: Isolation and characterization of novel lytic bacteriophages that infect multi drug resistant clinical strains of Escherichia coli.

Padmesh, Sudhakar / Singh, Aditi / Chopra, Sidharth / Sen, Manodeep / Habib, Saman / Shrivastava, Deepti / Johri, Parul

Environmental science and pollution research international

2023

Abstract: The pathogenic strains of Escherichia coli (E. coli) are frequent cause of urinary tract infections including catheter-associated, soft tissue infections and sepsis. The growing antibiotic resistance in E. coli is a major health concern. Bacteriophages ... ...

Abstract	The pathogenic strains of Escherichia coli (E. coli) are frequent cause of urinary tract infections including catheter-associated, soft tissue infections and sepsis. The growing antibiotic resistance in E. coli is a major health concern. Bacteriophages are specific for their bacterial host, thus providing a novel and effective alternatives. This study focuses on isolation of bacteriophages from urban sewage treatment plants. Initially 50 different bacteriophages have been isolated against non-resistant reference E. coli strain and fifty multidrug resistant clinical isolates of extraintestinal infections. Out of which only thirty-one lytic phages which gave clear plaques were further analysed for different physico-chemical aspects such as thermal inactivation, pH, effect of organic solvents and detergents. Two bacteriophages, ASEC2201 and ASEC2202, were selected for their ability to withstand temperature fluctuation from -20 to 62 °C and a pH range from 4 to 10. They also showed good survival (40-94%) in the presence of organic solvents like ethanol, acetone, DMSO and chloroform or ability to form plaques even after the treatment with detergents like SDS, CTAB and sarkosyl. Both efficiently killed reference strain and 40-44% of multidrug resistant clinical isolates of E. coli. Later ASEC2201 and ASEC2202 were subjected to morphological characterisation through transmission electron microscopy, which revealed them to be tailed phages. The genomic analysis confirmed them to be Escherichia phages which belonged to family Drexlerviridae of Caudovirales.
Language	English
Publishing date	2023-06-22
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-023-28081-z
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Book ; Online: APOBEC3B and ACE1 in-del polymorphisms as prima facie candidates for protection from COVID-19

Habib, Saman / Mukerji, Mitali

2020

Abstract: Population-specific differences in mortality are becoming evident after several months of the COVID-19 pandemic. This is despite differences in the extent of disease prevalence- China reported a fatality rate of ~5%, India ~ 3.3 %, with parts of Europe ... ...

Abstract	Population-specific differences in mortality are becoming evident after several months of the COVID-19 pandemic. This is despite differences in the extent of disease prevalence- China reported a fatality rate of ~5%, India ~ 3.3 %, with parts of Europe seeing much higher rates (~11 to 15%). Factors including demographics (elderly populations), containment responses, co-morbidities, quality of health care and other confounders could enhance differences in reported fatality rates. Within India, COVID-19 displays a skewed distribution with some states from Western and Central India reporting much higher numbers. An inverse relation of the overall number of cases infected with coronaviruses (i.e., MERS, SARS and COVID-19) and malaria across continental populations has been recently reported. A long history of exposure to malaria could have led to accumulation of genetic variants that confer protection to populations in disease-endemic regions. Here we highlight how signatures of selection in populations from malaria endemic regions can identify genetic variants that could modulate COVID-19 morbidity.
Keywords	covid19
Publisher	Center for Open Science
Publishing country	us
Document type	Book ; Online
DOI	10.31219/osf.io/6sfw8
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Article: YihA GTPases localize to the apicoplast and mitochondrion of the malaria parasite and interact with LSU of organellar ribosomes

Gupta, Ankit / Gupta, Kirti / Habib, Saman

Molecular and biochemical parasitology. 2020 Mar., v. 236

2020

Abstract: The YihA TRAFAC GTPases are critical for late-stage assembly of the ribosomal large subunit (LSU). In order to explore biogenesis of the reduced organellar ribosomes of the malaria parasite, we identified three nuclear-encoded homologs of YihA in ... ...

Abstract	The YihA TRAFAC GTPases are critical for late-stage assembly of the ribosomal large subunit (LSU). In order to explore biogenesis of the reduced organellar ribosomes of the malaria parasite, we identified three nuclear-encoded homologs of YihA in Plasmodium falciparum. PfYihA1 targeted to the parasite apicoplast, PfYihA2 to the mitochondrion, and PfYihA3 was found in both the apicoplast and cytosol. The three PfYihA, expressed as recombinant proteins, were active GTPases and interacted with surrogate E. coli ribosomes in a nucleotide-independent manner. In vivo complexation of PfYihA with parasite organellar and/or cytosolic LSU was confirmed by co-immunoprecipitation using specific antibodies. Mitochondrial PfYihA2 carries a large C-ter extension with a strongly positively charged stretch. We hypothesise that this is important in compensating for the absence of helices of the central protuberance in the fragmented rRNA of Plasmodium mitoribosomes and may provide additional contact sites to aid in complex assembly. Combined with previous reports, our results indicate that P. falciparum mitochondria are likely to assemble ribosomes with the aid of PfEngA, PfObg1 and PfYihA2 GTPases while apicoplast ribosomes might use PfYihA1 and 3 in combination with other factors.
Keywords	Escherichia coli ; Plasmodium falciparum ; antibodies ; biogenesis ; cytosol ; guanosinetriphosphatase ; malaria ; mitochondria ; parasites ; precipitin tests ; recombinant proteins ; ribosomal RNA ; ribosomes
Language	English
Dates of publication	2020-03
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	756166-0
ISSN	1872-9428 ; 0166-6851
ISSN (online)	1872-9428
ISSN	0166-6851
DOI	10.1016/j.molbiopara.2020.111265
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Article ; Online: YihA GTPases localize to the apicoplast and mitochondrion of the malaria parasite and interact with LSU of organellar ribosomes.

Gupta, Ankit / Gupta, Kirti / Habib, Saman

Molecular and biochemical parasitology

2020 Volume 236, Page(s) 111265

Abstract	The YihA TRAFAC GTPases are critical for late-stage assembly of the ribosomal large subunit (LSU). In order to explore biogenesis of the reduced organellar ribosomes of the malaria parasite, we identified three nuclear-encoded homologs of YihA in Plasmodium falciparum. PfYihA1 targeted to the parasite apicoplast, PfYihA2 to the mitochondrion, and PfYihA3 was found in both the apicoplast and cytosol. The three PfYihA, expressed as recombinant proteins, were active GTPases and interacted with surrogate E. coli ribosomes in a nucleotide-independent manner. In vivo complexation of PfYihA with parasite organellar and/or cytosolic LSU was confirmed by co-immunoprecipitation using specific antibodies. Mitochondrial PfYihA2 carries a large C-ter extension with a strongly positively charged stretch. We hypothesise that this is important in compensating for the absence of helices of the central protuberance in the fragmented rRNA of Plasmodium mitoribosomes and may provide additional contact sites to aid in complex assembly. Combined with previous reports, our results indicate that P. falciparum mitochondria are likely to assemble ribosomes with the aid of PfEngA, PfObg1 and PfYihA2 GTPases while apicoplast ribosomes might use PfYihA1 and 3 in combination with other factors.
MeSH term(s)	Apicoplasts/metabolism ; GTP Phosphohydrolases/metabolism ; GTP-Binding Proteins/metabolism ; Mitochondria/metabolism ; Mitochondrial Ribosomes ; Plasmodium/genetics ; Plasmodium/metabolism ; Protozoan Proteins/metabolism ; RNA, Ribosomal ; Ribosome Subunits, Large/metabolism
Chemical Substances	Protozoan Proteins ; RNA, Ribosomal ; GTP Phosphohydrolases (EC 3.6.1.-) ; GTP-Binding Proteins (EC 3.6.1.-)
Language	English
Publishing date	2020-02-11
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	756166-0
ISSN	1872-9428 ; 0166-6851
ISSN (online)	1872-9428
ISSN	0166-6851
DOI	10.1016/j.molbiopara.2020.111265
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Article ; Online: Plasmodium Ape1 is a multifunctional enzyme in mitochondrial base excision repair and is required for efficient transition from liver to blood stage infection.

Verma, Neetu / Shukla, Himadri / Tiwari, Anupama / Mishra, Satish / Habib, Saman

DNA repair

2021 Volume 101, Page(s) 103098

Abstract: The malaria parasite has a single mitochondrion which carries multiple tandem repeats of its 6 kb genome encoding three proteins of the electron transport chain. There is little information about DNA repair mechanisms for mitochondrial genome maintenance ...

Abstract	The malaria parasite has a single mitochondrion which carries multiple tandem repeats of its 6 kb genome encoding three proteins of the electron transport chain. There is little information about DNA repair mechanisms for mitochondrial genome maintenance in Plasmodium spp. Of the two AP-endonucleases of the BER pathway encoded in the parasite nuclear genome, the EndoIV homolog PfApn1 has been identified as a mitochondrial protein with restricted functions. We explored the targeting and biochemical properties of the ExoIII homolog PfApe1. PfApe1 localized in the mitochondrion and exhibited AP-site cleavage, 3'-5' exonuclease, 3'-phosphatase, nucleotide incision repair (NIR) and RNA cleavage activities indicating a wider functional role than PfApn1. The parasite enzyme differed from human APE1 in possessing a large, disordered N-terminal extension. Molecular modelling revealed conservation of structural domains but variations in DNA-interacting residues and an insertion in the α-8 loop suggested differences with APE1. Unlike APE1, where AP-site cleavage and NIR activities could be mutually exclusive based on pH and Mg
MeSH term(s)	Animals ; DNA/metabolism ; DNA Damage ; DNA Repair ; DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; Humans ; Kinetics ; Life Cycle Stages ; Malaria, Falciparum ; Mice ; Mitochondria/enzymology ; Mitochondria/genetics ; Models, Molecular ; Multifunctional Enzymes ; Plasmodium berghei ; Plasmodium falciparum/enzymology ; Plasmodium falciparum/genetics ; Plasmodium falciparum/growth & development ; Protein Conformation ; Substrate Specificity
Chemical Substances	Multifunctional Enzymes ; DNA (9007-49-2) ; DNA-(Apurinic or Apyrimidinic Site) Lyase (EC 4.2.99.18)
Language	English
Publishing date	2021-03-14
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2021.103098
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Article: PfKsgA1 functions as a transcription initiation factor and interacts with the N-terminal region of the mitochondrial RNA polymerase of Plasmodium falciparum

Gupta, Ankit / Shrivastava, Deepti / Shakya, Anil Kumar / Gupta, Kirti / Pratap, JV / Habib, Saman

Australian Society for Parasitology International journal for parasitology. 2021 Jan., v. 51, no. 1

2021

Abstract: The small mitochondrial genome (mtDNA) of the malaria parasite is known to transcribe its genes polycistonically, although promoter element(s) have not yet been identified. An unusually large Plasmodium falciparum candidate mitochondrial phage-like RNA ... ...

Abstract	The small mitochondrial genome (mtDNA) of the malaria parasite is known to transcribe its genes polycistonically, although promoter element(s) have not yet been identified. An unusually large Plasmodium falciparum candidate mitochondrial phage-like RNA polymerase (PfmtRNAP) with an extended N-terminal region is encoded by the parasite nuclear genome. Using specific antibodies against the enzyme, we established that PfmtRNAP was targeted exclusively to the mitochondrion and interacted with mtDNA. Phylogenetic analysis showed that it is part of a separate apicomplexan clade. A search for PfmtRNAP-associated transcription initiation factors using sequence homology and in silico protein–protein interaction network analysis identified PfKsgA1. PfKsgA1 is a dual cytosol- and mitochondrion-targeted protein that functions as a small subunit rRNA dimethyltransferase in ribosome biogenesis. Chromatin immunoprecipitation showed that PfKsgA1 interacts with mtDNA, and in vivo crosslinking and pull-down experiments confirmed PfmtRNAP-PfKsgA1 interaction. The ability of PfKsgA1 to serve as a transcription initiation factor was demonstrated by complementation of yeast mitochondrial transcription factor Mtf1 function in Rpo41-driven in vitro transcription. Pull-down experiments using PfKsgA1 and PfmtRNAP domains indicated that the N-terminal region of PfmtRNAP interacts primarily with the PfKsgA1 C-terminal domain with some contacts being made with the linker and N-terminal domain of PfKsgA1. In the absence of full-length recombinant PfmtRNAP, solution structures of yeast mitochondrial RNA polymerase Rpo41 complexes with Mtf1 or PfKsgA1 were determined by small-angle X-ray scattering. Protein interaction interfaces thus identified matched with those reported earlier for Rpo41-Mtf1 interaction and overlaid with the PfmtRNAP-interfacing region identified experimentally for PfKsgA1. Our results indicate that in addition to a role in mitochondrial ribosome biogenesis, PfKsgA1 has an independent function as a transcription initiation factor for PfmtRNAP.
Keywords	DNA-directed RNA polymerase ; Plasmodium falciparum ; amino acid sequences ; biogenesis ; chromatin immunoprecipitation ; computer simulation ; crosslinking ; malaria ; mitochondria ; mitochondrial RNA ; mitochondrial genome ; nuclear genome ; parasites ; parasitology ; phylogeny ; promoter regions ; protein-protein interactions ; ribosomes ; sequence homology ; small-angle X-ray scattering ; transcription factors ; transcription initiation ; yeasts
Language	English
Dates of publication	2021-01
Size	p. 23-37.
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	120518-3
ISSN	1879-0135 ; 0020-7519
ISSN (online)	1879-0135
ISSN	0020-7519
DOI	10.1016/j.ijpara.2020.07.010
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Article ; Online: Plasmodium falciparum FIKK9.1 is a monomeric serine-threonine protein kinase with features to exploit as a drug target.

D, Anil Kumar / Shrivastava, Deepti / Sahasrabuddhe, Amogh A / Habib, Saman / Trivedi, Vishal

Chemical biology & drug design

2021 Volume 97, Issue 4, Page(s) 962–977

Abstract: FIKK-9.1 is essential for parasite survival, but its structural and biochemical characterization will enable us to understand its role in the parasite life cycle. The recombinant FIKK9.1 kinase is monomeric with a native molecular weight of 60 ± 1.6 kDa. ...

Abstract	FIKK-9.1 is essential for parasite survival, but its structural and biochemical characterization will enable us to understand its role in the parasite life cycle. The recombinant FIKK9.1 kinase is monomeric with a native molecular weight of 60 ± 1.6 kDa. Structural characterization of FIKK9.1 kinase reveals that it consists of two domains: N-terminal FHA like domain and C-terminal kinase domain. The C-terminal domain has a well-defined pocket, but it displayed RMSD deviation of 1.38-3.2 Å from host kinases. ITC analysis indicates that ATP binds to the protein with a K
MeSH term(s)	Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; Molecular Dynamics Simulation ; Mutagenesis, Site-Directed ; Peptides/chemistry ; Peptides/metabolism ; Plasmodium falciparum/enzymology ; Protein Structure, Secondary ; Protein-Serine-Threonine Kinases/antagonists & inhibitors ; Protein-Serine-Threonine Kinases/genetics ; Protein-Serine-Threonine Kinases/metabolism ; Protozoan Proteins/antagonists & inhibitors ; Protozoan Proteins/genetics ; Protozoan Proteins/metabolism ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/chemistry ; Recombinant Proteins/isolation & purification ; Sequence Alignment ; Substrate Specificity
Chemical Substances	Peptides ; Protozoan Proteins ; Recombinant Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2021-01-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2216600-2
ISSN	1747-0285 ; 1747-0277
ISSN (online)	1747-0285
ISSN	1747-0277
DOI	10.1111/cbdd.13821
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Article: Characterization of mitochondrion-targeted GTPases in Plasmodium falciparum

Gupta, Kirti / Gupta, Ankit / Haider, Afreen / Habib, Saman

Parasitology. 2018 Oct., v. 145, no. 12

2018

Abstract: Ribosome assembly is critical for translation and regulating the response to cellular events and requires a complex interplay of ribosomal RNA and proteins with assembly factors. We investigated putative participants in the biogenesis of the reduced ... ...

Abstract	Ribosome assembly is critical for translation and regulating the response to cellular events and requires a complex interplay of ribosomal RNA and proteins with assembly factors. We investigated putative participants in the biogenesis of the reduced organellar ribosomes of Plasmodium falciparum and identified homologues of two assembly GTPases – EngA and Obg that were found in mitochondria. Both are indispensable in bacteria and P. berghei EngA is among the ‘essential’ parasite blood stage proteins identified recently. PfEngA and PfObg1 interacted with parasite mitoribosomes in vivo. GTP stimulated PfEngA interaction with the 50S subunit of Escherichia coli surrogate ribosomes. Although PfObg1–ribosome interaction was independent of nucleotide binding, GTP hydrolysis by PfObg1 was enhanced upon ribosomal association. An additional function for PfObg1 in mitochondrial DNA transactions was suggested by its specific interaction with the parasite mitochondrial genome in vivo. Deletion analysis revealed that the positively-charged OBG (spoOB-associated GTP-binding protein) domain mediates DNA-binding. A role for PfEngA in mitochondrial genotoxic stress response was indicated by its over-expression upon methyl methanesulfonate-induced DNA damage. PfEngA had lower sensitivity to an E. coli EngA inhibitor suggesting differences with bacterial counterparts. Our results show the involvement of two important GTPases in P. falciparum mitochondrial function, with the first confirmed localization of an EngA homologue in eukaryotic mitochondria.
Keywords	DNA damage ; Escherichia coli ; Plasmodium berghei ; Plasmodium falciparum ; bacteria ; biogenesis ; blood ; gene overexpression ; guanosine triphosphate ; guanosinetriphosphatase ; hydrolysis ; mitochondria ; mitochondrial DNA ; mitochondrial genome ; mutagens ; parasites ; proteins ; ribosomal RNA ; ribosomes ; stress response ; translation (genetics)
Language	English
Dates of publication	2018-10
Size	p. 1600-1612.
Publishing place	Cambridge University Press
Document type	Article
ZDB-ID	207627-5
ISSN	1469-8161 ; 0031-1820
ISSN (online)	1469-8161
ISSN	0031-1820
DOI	10.1017/S0031182018000501
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