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  1. Article ; 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.
    Language English
    Publishing date 2022-10-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 619315-8
    ISSN 1365-2958 ; 0950-382X
    ISSN (online) 1365-2958
    ISSN 0950-382X
    DOI 10.1111/mmi.14991
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  2. Article ; Online: Regulation of mRNA decay in

    Mohanty, Bijoy K / Kushner, Sidney R

    Critical reviews in biochemistry and molecular biology

    2021  Volume 57, Issue 1, Page(s) 48–72

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

    Abstract Detailed studies of the Gram-negative model bacterium,
    MeSH term(s) Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial ; RNA Stability/physiology ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Ribonucleases/metabolism
    Chemical Substances RNA, Bacterial ; RNA, Messenger ; Ribonucleases (EC 3.1.-)
    Language English
    Publishing date 2021-09-21
    Publishing country England
    Document type 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. Article ; Online: Inactivation of RNase P in Escherichia coli significantly changes post-transcriptional RNA metabolism.

    Mohanty, Bijoy K / Kushner, Sidney R

    Molecular microbiology

    2021  Volume 117, Issue 1, Page(s) 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 term(s) 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
    Chemical Substances 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.-)
    Language English
    Publishing date 2021-09-25
    Publishing country England
    Document type 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. Article ; 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  Volume 118, Issue 1-2, Page(s) 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 term(s) 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
    Chemical Substances 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)
    Language English
    Publishing date 2022-06-13
    Publishing country England
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: New Insights into the Relationship between tRNA Processing and Polyadenylation in Escherichia coli.

    Mohanty, Bijoy K / Kushner, Sidney R

    Trends in genetics : TIG

    2019  Volume 35, Issue 6, Page(s) 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 term(s) 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
    Chemical Substances RNA, Messenger ; RNA, Transfer (9014-25-9) ; Exoribonucleases (EC 3.1.-)
    Language English
    Publishing date 2019-04-26
    Publishing country England
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; 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  Volume 50, Issue 3, Page(s) 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 term(s) Endoribonucleases/genetics ; Endoribonucleases/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Nucleotides/metabolism ; RNA Precursors/metabolism ; RNA, Transfer, Pro/metabolism
    Chemical Substances Nucleotides ; RNA Precursors ; RNA, Transfer, Pro ; Endoribonucleases (EC 3.1.-) ; ribonuclease E (EC 3.1.4.-)
    Language English
    Publishing date 2021-12-15
    Publishing country England
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Analysis of post-transcriptional RNA metabolism in prokaryotes.

    Mohanty, Bijoy K / Kushner, Sidney R

    Methods (San Diego, Calif.)

    2018  Volume 155, Page(s) 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 term(s) 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
    Chemical Substances DNA, Complementary ; RNA, Bacterial ; RNA, Messenger ; RNA, Transfer (9014-25-9) ; Deoxyribonuclease I (EC 3.1.21.1)
    Language English
    Publishing date 2018-11-15
    Publishing country United States
    Document type 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; 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  Volume 12, Issue 37, Page(s) 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
    Language English
    Publishing date 2020-09-03
    Publishing country United States
    Document type Journal Article
    ISSN 1944-8252
    ISSN (online) 1944-8252
    DOI 10.1021/acsami.0c13690
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  9. Article ; 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  Volume 48, Issue 5, Page(s) 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 term(s) 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
    Chemical Substances RNA Precursors ; RNA, Bacterial ; RNA, Messenger ; Poly A (24937-83-5) ; Ribonuclease P (EC 3.1.26.5)
    Language English
    Publishing date 2020-01-24
    Publishing country England
    Document type 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
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  10. Article ; Online: Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria.

    Mohanty, Bijoy K / Kushner, Sidney R

    Microbiology spectrum

    2018  Volume 6, Issue 2

    Abstract: Gene expression in Gram-negative bacteria is regulated at many levels, including transcription initiation, RNA processing, RNA/RNA interactions, mRNA decay, and translational controls involving enzymes that alter translational efficiency. In this review, ...

    Abstract Gene expression in Gram-negative bacteria is regulated at many levels, including transcription initiation, RNA processing, RNA/RNA interactions, mRNA decay, and translational controls involving enzymes that alter translational efficiency. In this review, we discuss the various enzymes that control transcription, translation, and RNA stability through RNA processing and degradation. RNA processing is essential to generate functional RNAs, while degradation helps control the steady-state level of each individual transcript. For example, all the pre-tRNAs are transcribed with extra nucleotides at both their 5' and 3' termini, which are subsequently processed to produce mature tRNAs that can be aminoacylated. Similarly, rRNAs that are transcribed as part of a 30S polycistronic transcript are matured to individual 16S, 23S, and 5S rRNAs. Decay of mRNAs plays a key role in gene regulation through controlling the steady-state level of each transcript, which is essential for maintaining appropriate protein levels. In addition, degradation of both translated and nontranslated RNAs recycles nucleotides to facilitate new RNA synthesis. To carry out all these reactions, Gram-negative bacteria employ a large number of endonucleases, exonucleases, RNA helicases, and poly(A) polymerase, as well as proteins that regulate the catalytic activity of particular RNases. Under certain stress conditions, an additional group of specialized endonucleases facilitate the cell's ability to adapt and survive. Many of the enzymes, such as RNase E, RNase III, polynucleotide phosphorylase, RNase R, and poly(A) polymerase I, participate in multiple RNA processing and decay pathways.
    MeSH term(s) Bacterial Toxins/metabolism ; Bacteriocins/metabolism ; CRISPR-Cas Systems ; Endonucleases/metabolism ; Endoribonucleases/metabolism ; Exonucleases/metabolism ; Exoribonucleases/metabolism ; Gene Expression Regulation, Bacterial ; Gram-Negative Bacteria/enzymology ; Polyribonucleotide Nucleotidyltransferase/metabolism ; RNA Helicases/metabolism ; RNA Processing, Post-Transcriptional/physiology ; RNA Stability ; RNA, Bacterial/metabolism ; RNA, Messenger/metabolism ; RNA, Transfer/metabolism ; RNA, Untranslated/metabolism ; Ribonuclease III/metabolism
    Chemical Substances Bacterial Toxins ; Bacteriocins ; RNA, Bacterial ; RNA, Messenger ; RNA, Untranslated ; RNA, Transfer (9014-25-9) ; Polyribonucleotide Nucleotidyltransferase (EC 2.7.7.8) ; Endonucleases (EC 3.1.-) ; Endoribonucleases (EC 3.1.-) ; Exonucleases (EC 3.1.-) ; Exoribonucleases (EC 3.1.-) ; Ribonuclease III (EC 3.1.26.3) ; ribonuclease R (EC 3.1.27.-) ; ribonuclease E (EC 3.1.4.-) ; RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2018-04-19
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/microbiolspec.RWR-0011-2017
    Database MEDical Literature Analysis and Retrieval System OnLINE

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