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  1. Artikel ; Online: Processing of the alaW alaX operon encoding the Ala2 tRNAs in Escherichia coli requires both RNase E and RNase P.

    Mohanty, Bijoy K / Kushner, Sidney R

    Molecular microbiology

    2022  

    Abstract: The alaW alaX operon encodes the Ala2 tRNAs, one of the two alanine tRNA isotypes in Escherichia coli. Our previous RNA-seq study showed that alaW alaX dicistronic RNA levels increased significantly in the absence of both RNase P and poly(A) polymerase I ...

    Abstract The alaW alaX operon encodes the Ala2 tRNAs, one of the two alanine tRNA isotypes in Escherichia coli. Our previous RNA-seq study showed that alaW alaX dicistronic RNA levels increased significantly in the absence of both RNase P and poly(A) polymerase I (PAP I), suggesting a role of polyadenylation in its stability. In this report, we show that RNase E initiates the processing of the primary alaW alaX precursor RNA by removing the Rho-independent transcription terminator, which appears to be the rate limiting step in the separation and maturation of the Ala2 pre-tRNAs by RNase P. Failure to separate the alaW and alaX pre-tRNAs by RNase P leads to poly(A)-mediated degradation of the dicistronic RNAs by polynucleotide phosphorylase (PNPase) and RNase R. Surprisingly, the thermosensitive RNase E encoded by the rne-1 allele is highly efficient in removing the terminator (>99%) at the nonpermissive temperature suggesting a significant caveat in experiments using this allele. Together, our data present a comprehensive picture of the Ala2 tRNA processing pathway and demonstrate that unprocessed RNase P substrates are degraded via a poly(A) mediated decay pathway.
    Sprache Englisch
    Erscheinungsdatum 2022-10-21
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 619315-8
    ISSN 1365-2958 ; 0950-382X
    ISSN (online) 1365-2958
    ISSN 0950-382X
    DOI 10.1111/mmi.14991
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Regulation of mRNA decay in

    Mohanty, Bijoy K / Kushner, Sidney R

    Critical reviews in biochemistry and molecular biology

    2021  Band 57, Heft 1, Seite(n) 48–72

    Abstract: Detailed studies of the Gram-negative model bacterium, ...

    Abstract Detailed studies of the Gram-negative model bacterium,
    Mesh-Begriff(e) Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial ; RNA Stability/physiology ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Ribonucleases/metabolism
    Chemische Substanzen RNA, Bacterial ; RNA, Messenger ; Ribonucleases (EC 3.1.-)
    Sprache Englisch
    Erscheinungsdatum 2021-09-21
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1000977-2
    ISSN 1549-7798 ; 1381-3455 ; 1040-9238
    ISSN (online) 1549-7798
    ISSN 1381-3455 ; 1040-9238
    DOI 10.1080/10409238.2021.1968784
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  3. Artikel ; Online: Inactivation of RNase P in Escherichia coli significantly changes post-transcriptional RNA metabolism.

    Mohanty, Bijoy K / Kushner, Sidney R

    Molecular microbiology

    2021  Band 117, Heft 1, Seite(n) 121–142

    Abstract: Ribonuclease P (RNase P), which is required for the 5'-end maturation of tRNAs in every organism, has been shown to play a limited role in other aspects of RNA metabolism in Escherichia coli. Using RNA-sequencing (RNA-seq), we demonstrate that RNase P ... ...

    Abstract Ribonuclease P (RNase P), which is required for the 5'-end maturation of tRNAs in every organism, has been shown to play a limited role in other aspects of RNA metabolism in Escherichia coli. Using RNA-sequencing (RNA-seq), we demonstrate that RNase P inactivation affects the abundances of ~46% of the expressed transcripts in E. coli and provide evidence that its essential function is its ability to generate pre-tRNAs from polycistronic tRNA transcripts. The RNA-seq results agreed with the published data and northern blot analyses of 75/83 transcripts (mRNAs, sRNAs, and tRNAs). Changes in transcript abundances in the RNase P mutant also correlated with changes in their half-lives. Inactivating the stringent response did not alter the rnpA49 phenotype. Most notably, increases in the transcript abundances were observed for all genes in the cysteine regulons, multiple toxin-antitoxin modules, and sigma S-controlled genes. Surprisingly, poly(A) polymerase (PAP I) modulated the abundances of ~10% of the transcripts affected by RNase P. A comparison of the transcriptomes of RNase P, RNase E, and RNase III mutants suggests that they affect distinct substrates. Together, our work strongly indicates that RNase P is a major player in all aspects of post-transcriptional RNA metabolism in E. coli.
    Mesh-Begriff(e) Endoribonucleases/genetics ; Endoribonucleases/metabolism ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Gene Expression Regulation, Bacterial ; RNA Precursors/genetics ; RNA Precursors/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism ; RNA, Messenger/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Regulon/genetics ; Ribonuclease III/genetics ; Ribonuclease III/metabolism ; Ribonuclease P/genetics ; Ribonuclease P/metabolism ; Sequence Analysis, RNA ; Transcriptome
    Chemische Substanzen Escherichia coli Proteins ; RNA Precursors ; RNA, Bacterial ; RNA, Messenger ; RNA, Transfer (9014-25-9) ; Endoribonucleases (EC 3.1.-) ; Ribonuclease III (EC 3.1.26.3) ; Ribonuclease P (EC 3.1.26.5) ; ribonuclease E (EC 3.1.4.-)
    Sprache Englisch
    Erscheinungsdatum 2021-09-25
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 619315-8
    ISSN 1365-2958 ; 0950-382X
    ISSN (online) 1365-2958
    ISSN 0950-382X
    DOI 10.1111/mmi.14808
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  4. Artikel ; Online: Maturation of the E. coli Glu2, Ile1, and Ala1B tRNAs utilizes a complex processing pathway.

    Mohanty, Bijoy K / Nichols, Keri / Kushner, Sidney R

    Molecular microbiology

    2022  Band 118, Heft 1-2, Seite(n) 30–46

    Abstract: Despite significant progress in understanding the diversity of tRNA processing pathways in Escherichia coli, the mechanism for the maturation of tRNAs encoded within the rRNA operons has not received much attention. Here, we show that the Glu2, Ile1, and ...

    Abstract Despite significant progress in understanding the diversity of tRNA processing pathways in Escherichia coli, the mechanism for the maturation of tRNAs encoded within the rRNA operons has not received much attention. Here, we show that the Glu2, Ile1, and Ala1B tRNAs, encoded by 10 genes located between the 16S and 23S rRNAs in the seven rRNA operons, are matured via a RNase E-independent processing pathway that utilizes at least six different enzymes. It has been shown that the Glu2 and Ile1-Ala1B pre-tRNAs released by initial RNase III cleavages of the 30S primary rRNA transcripts retain extended 5'-leader (35-139 nt) and 3'-trailer (166-185 nt) sequences. However, the 5' maturation of the tRNAs by RNase P is inhibited until the trailer sequences are shortened to 1-4 nucleotides, initially by a second RNase III cleavage at 31-42 nucleotides downstream of the CCA determinant followed by exonucleolytic trimming. The RNase III cleaved Glu2 and Ile1-Ala1B trailer fragments are degraded via PAP I- dependent exonucleolytic decay. Compared to the six previously characterized tRNA processing pathways, maturation of the Glu2, Ile1, and Ala1B tRNAs is considerably more complex and appears to be distinct from what occurs in Gram-positive bacteria.
    Mesh-Begriff(e) Endoribonucleases/metabolism ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Nucleotides/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Ribonuclease III/metabolism ; Ribonuclease P/genetics ; Ribonuclease P/metabolism
    Chemische Substanzen Escherichia coli Proteins ; Nucleotides ; RNA, Bacterial ; RNA, Transfer (9014-25-9) ; Endoribonucleases (EC 3.1.-) ; Ribonuclease III (EC 3.1.26.3) ; Ribonuclease P (EC 3.1.26.5)
    Sprache Englisch
    Erscheinungsdatum 2022-06-13
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 619315-8
    ISSN 1365-2958 ; 0950-382X
    ISSN (online) 1365-2958
    ISSN 0950-382X
    DOI 10.1111/mmi.14949
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  5. Artikel ; Online: Biocompatible polymer-coated magneto-fluorescent super nanoparticles for the homing of mesenchymal stem cells.

    Dash, Saumya / Majood, Misba / Meena, Ravindra / Mukherjee, Monalisa / Dinda, Amit K / Kuanr, Bijoy K / Mohanty, Sujata

    International journal of biological macromolecules

    2024  , Seite(n) 132794

    Abstract: Stem cell plays an important role in the clinical field. However, the effective delivery of stem cells to the targeted site relies on the efficient homing of the cells to the site of injury. In view of that, fluorescent magnetic nanoparticles stick out ... ...

    Abstract Stem cell plays an important role in the clinical field. However, the effective delivery of stem cells to the targeted site relies on the efficient homing of the cells to the site of injury. In view of that, fluorescent magnetic nanoparticles stick out due to their wide range of enabling functions including cellular homing and tracking. The present study unravels the synthesis of polymer-coated biocompatible and fluorescent magnetic nanoparticles (FMNPs) by a single-step hydrothermal synthesis method. Importantly, the facile method developed the biological super nanoparticles consisting of the magnetic core, which is surrounded by the fluorescent nanodot-decorated polymeric shell. The synthesized particles showed an amorphous nature, and superparamagnetic properties, with efficient fluorescence properties of emission at the blue range (̴ 410 nm). The FMNP labeling showed the mesenchymal stem cell (MSC) homing to the desired site in the presence of an external magnetic field. The in-house synthesized nanoparticles showed significant cytocompatibility and hemocompatibility in vitro as well as in vivo conditions owing to their surface coating. This unprecedented work advances the efficient internalization of FMNPs in MSCs and their enhanced migration potential provides a breakthrough in stem cell delivery for therapeutic applications. STATEMENT OF SIGNIFICANCE: The bi-modal fluorescent magnetic nanoparticles hold a promising role in the biomedical field for mesenchymal stem cell homing and tracking. Hence, in this study, for the first time, we have synthesized the fluorescent magnetic nanoparticle with polymer coating via an easy single-step method. The nanoparticle with a polymer coat enhanced the biocompatibility and effortless internalization of the nanoparticle into mesenchymal stem cells without hampering the native stem cell properties. Furthermore, the enhanced migration potential of such magnetized stem cells and their homing at the target site by applying an external magnetic field opened up avenues for the smart delivery of mesenchymal stem cells at complex sites such as retina for the tissue regeneration.
    Sprache Englisch
    Erscheinungsdatum 2024-06-02
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2024.132794
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  6. Artikel: New Insights into the Relationship between tRNA Processing and Polyadenylation in Escherichia coli.

    Mohanty, Bijoy K / Kushner, Sidney R

    Trends in genetics : TIG

    2019  Band 35, Heft 6, Seite(n) 434–445

    Abstract: Recent studies suggest that poly(A) polymerase I (PAP I)-mediated polyadenylation in Escherichia coli is highly prevalent among mRNAs as well as tRNA precursors. Primary tRNA transcripts are initially processed endonucleolytically to generate pre-tRNA ... ...

    Abstract Recent studies suggest that poly(A) polymerase I (PAP I)-mediated polyadenylation in Escherichia coli is highly prevalent among mRNAs as well as tRNA precursors. Primary tRNA transcripts are initially processed endonucleolytically to generate pre-tRNA species, which undergo 5'-end maturation by the ribozyme RNase P. Subsequently, a group of 3' → 5' exonucleases mature the 3' ends of the majority of tRNAs with few exceptions. PAP I competes with the 3' → 5' exonucleases for pre-tRNA substrates adding short poly(A) tails, which not only modulate the stability of the pre-tRNAs, but also regulate the availability of functional tRNAs. In this review, we discuss the recent discoveries of new tRNA processing pathways and the implications of polyadenylation in tRNA metabolism in E. coli.
    Mesh-Begriff(e) Animals ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Exoribonucleases/metabolism ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Humans ; Polyadenylation ; Protein Binding ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics ; RNA, Transfer/genetics ; Signal Transduction
    Chemische Substanzen RNA, Messenger ; RNA, Transfer (9014-25-9) ; Exoribonucleases (EC 3.1.-)
    Sprache Englisch
    Erscheinungsdatum 2019-04-26
    Erscheinungsland England
    Dokumenttyp Journal Article ; Review
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2019.03.003
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: The C nucleotide at the mature 5' end of the Escherichia coli proline tRNAs is required for the RNase E cleavage specificity at the 3' terminus as well as functionality.

    Mohanty, Bijoy K / Maples, Valerie / Kushner, Sidney R

    Nucleic acids research

    2021  Band 50, Heft 3, Seite(n) 1639–1649

    Abstract: Proline tRNA 3'-maturation in Escherichia coli occurs through a one-step RNase E endonucleolytic cleavage immediately after the CCA determinant. This processing pathway is distinct from the 3'-end maturation of the other tRNAs by avoiding the widespread ... ...

    Abstract Proline tRNA 3'-maturation in Escherichia coli occurs through a one-step RNase E endonucleolytic cleavage immediately after the CCA determinant. This processing pathway is distinct from the 3'-end maturation of the other tRNAs by avoiding the widespread use of 3' → 5' exonucleolytic processing, 3'-polyadenylation and subsequent degradation. Here, we show that the cytosine (C) at the mature 5'-terminus of the proK and proL tRNAs is required for both the RNase E cleavage immediately after the CCA determinant and their functionality. Thus, changing the C nucleotide at the mature 5'-terminus of the proL and proK tRNAs to the more common G nucleotide led to RNase E cleavages 1-4 nucleotides downstream of the CCA determinant. Furthermore, the 5'-modified mutant tRNAs required RNase T and RNase PH for their 3'-maturation and became substrates for polyadenylation and degradation. Strikingly, the aminoacylation of the 5'-modified proline tRNAs was blocked due to the change in the recognition element for prolyl-tRNA-synthetase. An analogous modification of the pheV 5'-mature terminus from G to C nucleotide did not support cell viability. This result provides additional support for the importance of first nucleotide of the mature tRNAs in their processing and functionality.
    Mesh-Begriff(e) Endoribonucleases/genetics ; Endoribonucleases/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Nucleotides/metabolism ; RNA Precursors/metabolism ; RNA, Transfer, Pro/metabolism
    Chemische Substanzen Nucleotides ; RNA Precursors ; RNA, Transfer, Pro ; Endoribonucleases (EC 3.1.-) ; ribonuclease E (EC 3.1.4.-)
    Sprache Englisch
    Erscheinungsdatum 2021-12-15
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab1260
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  8. Artikel ; Online: Analysis of post-transcriptional RNA metabolism in prokaryotes.

    Mohanty, Bijoy K / Kushner, Sidney R

    Methods (San Diego, Calif.)

    2018  Band 155, Seite(n) 124–130

    Abstract: Post-transcriptional RNA metabolic pathways play important roles in permitting prokaryotes to operate under a variety of environmental conditions. Although significant progress has been made during the last decade in deciphering RNA processing pathways ... ...

    Abstract Post-transcriptional RNA metabolic pathways play important roles in permitting prokaryotes to operate under a variety of environmental conditions. Although significant progress has been made during the last decade in deciphering RNA processing pathways in a number of bacteria, a complete understanding of post-transcriptional RNA metabolism in any single microorganism is far from reality. Here we describe multiple experimental approaches that can be used to study mRNA stability, tRNA and rRNA processing, sRNA metabolism, and polyadenylation in prokaryotes. The methods described here can be readily utilized in both Gram-negative and Gram-positive bacteria with simple modifications.
    Mesh-Begriff(e) Base Sequence ; Blotting, Northern ; Cloning, Molecular ; DNA, Complementary/biosynthesis ; DNA, Complementary/genetics ; Denaturing Gradient Gel Electrophoresis ; Deoxyribonuclease I/chemistry ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Half-Life ; Polyadenylation ; RNA Processing, Post-Transcriptional ; RNA Stability ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Sequence Analysis, DNA/methods
    Chemische Substanzen DNA, Complementary ; RNA, Bacterial ; RNA, Messenger ; RNA, Transfer (9014-25-9) ; Deoxyribonuclease I (EC 3.1.21.1)
    Sprache Englisch
    Erscheinungsdatum 2018-11-15
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2018.11.006
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  9. Artikel ; Online: Tailoring the Design of a Lanthanide Complex/Magnetic Ferrite Nanocomposite for Efficient Photoluminescence and Magnetic Hyperthermia Performance.

    Das, Anindita / Mohanty, Sonali / Kumar, Ravi / Kuanr, Bijoy K

    ACS applied materials & interfaces

    2020  Band 12, Heft 37, Seite(n) 42016–42029

    Abstract: In this work, we have designed a magnetoluminescent nanocomposite as a single platform for optical imaging and safe magnetic hyperthermia therapy by optimizing the composition of magnetic nanoparticles and controlling the conjugation strategy of the ... ...

    Abstract In this work, we have designed a magnetoluminescent nanocomposite as a single platform for optical imaging and safe magnetic hyperthermia therapy by optimizing the composition of magnetic nanoparticles and controlling the conjugation strategy of the luminescent lanthanide complex. We have synthesized Co
    Sprache Englisch
    Erscheinungsdatum 2020-09-03
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 1944-8252
    ISSN (online) 1944-8252
    DOI 10.1021/acsami.0c13690
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  10. Artikel ; Online: Generation of pre-tRNAs from polycistronic operons is the essential function of RNase P in Escherichia coli.

    Mohanty, Bijoy K / Agrawal, Ankit / Kushner, Sidney R

    Nucleic acids research

    2020  Band 48, Heft 5, Seite(n) 2564–2578

    Abstract: Ribonuclease P (RNase P) is essential for the 5'-end maturation of tRNAs in all kingdoms of life. In Escherichia coli, temperature sensitive mutations in either its protein (rnpA49) and or RNA (rnpB709) subunits lead to inviability at nonpermissive ... ...

    Abstract Ribonuclease P (RNase P) is essential for the 5'-end maturation of tRNAs in all kingdoms of life. In Escherichia coli, temperature sensitive mutations in either its protein (rnpA49) and or RNA (rnpB709) subunits lead to inviability at nonpermissive temperatures. Using the rnpA49 temperature sensitive allele, which encodes a partially defective RNase P at the permissive temperature, we show here for the first time that the processing of RNase P-dependent polycistronic tRNA operons to release pre-tRNAs is the essential function of the enzyme, since the majority of 5'-immature tRNAs can be aminoacylated unless their 5'-extensions ≥8 nt. Surprisingly, the failure of 5'-end maturation elicits increased polyadenylation of some pre-tRNAs by poly(A) polymerase I (PAP I), which exacerbates inviability. The absence of PAP I led to improved aminoacylation of 5'-immature tRNAs. Our data suggest a more dynamic role for PAP I in maintaining functional tRNA levels in the cell.
    Mesh-Begriff(e) Aminoacylation ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli/growth & development ; Gene Expression Regulation, Bacterial ; Mutation/genetics ; Operon/genetics ; Poly A/metabolism ; RNA Precursors/biosynthesis ; RNA, Bacterial/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Ribonuclease P/metabolism
    Chemische Substanzen RNA Precursors ; RNA, Bacterial ; RNA, Messenger ; Poly A (24937-83-5) ; Ribonuclease P (EC 3.1.26.5)
    Sprache Englisch
    Erscheinungsdatum 2020-01-24
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkz1188
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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