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  1. Article ; Online: Hfq-Antisense RNA I Binding Regulates RNase E-Dependent RNA Stability and ColE1 Plasmid Copy Number.

    Wang, Wei-Syuan / Lin-Chao, Sue

    International journal of molecular sciences

    2024  Volume 25, Issue 7

    Abstract: The mechanisms and consequences of gene regulation by Hfq ... ...

    Abstract The mechanisms and consequences of gene regulation by Hfq on
    MeSH term(s) RNA, Antisense/genetics ; DNA Copy Number Variations ; Plasmids/genetics ; RNA Stability ; Endoribonucleases
    Chemical Substances RNA, Antisense ; ribonuclease E (EC 3.1.4.-) ; Endoribonucleases (EC 3.1.-)
    Language English
    Publishing date 2024-04-02
    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/ijms25073955
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  2. Article ; Online: Sodium Fluoride Exposure Leads to ATP Depletion and Altered RNA Decay in Escherichia coli under Anaerobic Conditions.

    Murashko, Oleg N / Yeh, Kun-Hai / Yu, Chen-Hsin Albert / Kaberdin, Vladimir R / Lin-Chao, Sue

    Microbiology spectrum

    2023  , Page(s) e0415822

    Abstract: Although fluoride-containing compounds are widely used to inhibit bacterial growth, the reprogramming of gene expression underlying cellular responses to fluoride, especially under anaerobic conditions, is still poorly understood. Here, we compare the ... ...

    Abstract Although fluoride-containing compounds are widely used to inhibit bacterial growth, the reprogramming of gene expression underlying cellular responses to fluoride, especially under anaerobic conditions, is still poorly understood. Here, we compare the genome-wide transcriptomic profiles of E. coli grown in the absence (control) or presence (20 and 70 mM) of sodium fluoride (NaF) under anaerobic conditions and assess the impact of fluoride-dependent ATP depletion on RNA turnover. Tiling array analysis revealed transcripts displaying altered abundance in response to NaF treatments. Quantile-based K-means clustering uncovered a subset of genes that were highly upregulated and then downregulated in response to increased and subsequently decreased fluoride concentrations, many of which (~40%) contained repetitive extragenic palindromic (REP) sequences. Northern blot analysis of some of these highly upregulated REP-containing transcripts (i.e.,
    Language English
    Publishing date 2023-03-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.04158-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Combined Transcriptomic and Proteomic Profiling of

    Liou, Gunn-Guang / Chao Kaberdina, Anna / Wang, Wei-Syuan / Kaberdin, Vladimir R / Lin-Chao, Sue

    International journal of molecular sciences

    2022  Volume 23, Issue 5

    Abstract: Adaptive mechanisms that facilitate intestinal colonization by the human microbiota, ... ...

    Abstract Adaptive mechanisms that facilitate intestinal colonization by the human microbiota, including
    MeSH term(s) Anaerobiosis ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Humans ; Iron/metabolism ; Membrane Proteins/metabolism ; Oxygen/metabolism ; Proteomics ; RNA, Untranslated/metabolism ; Transcriptome
    Chemical Substances Escherichia coli Proteins ; HdeD protein, E coli ; Membrane Proteins ; RNA, Untranslated ; Iron (E1UOL152H7) ; Oxygen (S88TT14065)
    Language English
    Publishing date 2022-02-25
    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/ijms23052570
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  4. Article ; Online: Posttranscriptional Regulation of

    Singh, Dharam / Murashko, Oleg N / Lin-Chao, Sue

    Journal of bacteriology

    2020  Volume 202, Issue 10

    Abstract: Escherichia ... ...

    Abstract Escherichia coli
    MeSH term(s) Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli/growth & development ; Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial ; Protein Binding ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism ; Ribosomal Proteins/genetics ; Ribosomal Proteins/metabolism ; Transcription, Genetic
    Chemical Substances RNA, Bacterial ; Ribosomal Proteins ; ribosomal protein L4
    Language English
    Publishing date 2020-04-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.00799-19
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  5. Article ; Online: Escherichia coli

    Murashko, Oleg N / Lin-Chao, Sue

    Proceedings of the National Academy of Sciences of the United States of America

    2017  Volume 114, Issue 38, Page(s) E8025–E8034

    Abstract: Escherichia ... ...

    Abstract Escherichia coli
    Language English
    Publishing date 2017-09-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1703731114
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  6. Article ; Online: Gas7 knockout affects PINK1 expression and mitochondrial dynamics in mouse cortical neurons.

    Bhupana, Jagannatham Naidu / Huang, Bo-Tsang / Liou, Gunn-Guang / Calkins, Marcus J / Lin-Chao, Sue

    FASEB bioAdvances

    2020  Volume 2, Issue 3, Page(s) 166–181

    Abstract: Dynamic fission and fusion events regulate mitochondrial shape, distribution, and rejuvenation, and proper control of these processes is essential for neuronal homeostasis. Here, we report that Gas7, a known cytoskeleton regulator, controls mitochondrial ...

    Abstract Dynamic fission and fusion events regulate mitochondrial shape, distribution, and rejuvenation, and proper control of these processes is essential for neuronal homeostasis. Here, we report that Gas7, a known cytoskeleton regulator, controls mitochondrial dynamics within neurons of the central nervous system. In this study, we generated an improved
    Language English
    Publishing date 2020-01-21
    Publishing country United States
    Document type Journal Article
    ISSN 2573-9832
    ISSN (online) 2573-9832
    DOI 10.1096/fba.2019-00091
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  7. Article ; Online: Correction to: Reprogramming of gene expression in Escherichia coli cultured on pyruvate versus glucose.

    Kaberdina, Anna Chao / Ruiz-Larrabeiti, Olatz / Lin-Chao, Sue / Kaberdin, Vladimir R

    Molecular genetics and genomics : MGG

    2019  Volume 294, Issue 5, Page(s) 1373

    Abstract: The article Reprogramming of. ...

    Abstract The article Reprogramming of.
    Language English
    Publishing date 2019-03-01
    Publishing country Germany
    Document type Published Erratum
    ZDB-ID 2044817-X
    ISSN 1617-4623 ; 1617-4615
    ISSN (online) 1617-4623
    ISSN 1617-4615
    DOI 10.1007/s00438-019-01603-6
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    Zs.A 1198: Show issues Location:
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  8. Article ; Online: Combined Transcriptomic and Proteomic Profiling of E. coli under Microaerobic versus Aerobic Conditions

    Gunn-Guang Liou / Anna Chao Kaberdina / Wei-Syuan Wang / Vladimir R. Kaberdin / Sue Lin-Chao

    International Journal of Molecular Sciences, Vol 23, Iss 2570, p

    The Multifaceted Roles of Noncoding Small RNAs and Oxygen-Dependent Sensing in Global Gene Expression Control

    2022  Volume 2570

    Abstract: Adaptive mechanisms that facilitate intestinal colonization by the human microbiota, including Escherichia coli , may be better understood by analyzing the physiology and gene expression of bacteria in low-oxygen environments. We used high-throughput ... ...

    Abstract Adaptive mechanisms that facilitate intestinal colonization by the human microbiota, including Escherichia coli , may be better understood by analyzing the physiology and gene expression of bacteria in low-oxygen environments. We used high-throughput transcriptomics and proteomics to compare the expression profiles of E. coli grown under aerobic versus microaerobic conditions. Clustering of high-abundance transcripts under microaerobiosis highlighted genes controlling acid-stress adaptation ( gadAXW , gadAB , hdeAB-yhiD and hdeD operons), cell adhesion/biofilm formation ( pgaABCD and csgDEFG operons), electron transport ( cydAB ), oligopeptide transport ( oppABCDF ), and anaerobic respiration/fermentation ( hyaABCDEF and hycABCDEFGHI operons). In contrast, downregulated genes were involved in iron transport ( fhuABCD , feoABC and fepA-entD operons), iron-sulfur cluster assembly ( iscRSUA and sufABCDSE operons), aerobic respiration ( sdhDAB and sucABCDSE operons), and de novo nucleotide synthesis ( nrdHIEF ). Additionally, quantitative proteomics showed that the products (proteins) of these high- or low-abundance transcripts were expressed consistently. Our findings highlight interrelationships among energy production, carbon metabolism, and iron homeostasis. Moreover, we have identified and validated a subset of differentially expressed noncoding small RNAs (i.e., CsrC, RyhB, RprA and GcvB), and we discuss their regulatory functions during microaerobic growth. Collectively, we reveal key changes in gene expression at the transcriptional and post-transcriptional levels that sustain E. coli growth when oxygen levels are low.
    Keywords transcriptional and post-transcriptional regulation ; iron homeostasis ; anaerobic respiration ; acid stress response ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 570
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Reprogramming of gene expression in Escherichia coli cultured on pyruvate versus glucose.

    Kaberdina, Anna Chao / Ruiz-Larrabeiti, Olatz / Lin-Chao, Sue / Kaberdin, Vladimir R

    Molecular genetics and genomics : MGG

    2019  Volume 294, Issue 5, Page(s) 1359–1371

    Abstract: Previous studies revealed important roles of small RNAs (sRNAs) in regulation of bacterial metabolism, stress responses and virulence. However, only a minor fraction of sRNAs is well characterized with respect to the spectra of their targets, conditional ...

    Abstract Previous studies revealed important roles of small RNAs (sRNAs) in regulation of bacterial metabolism, stress responses and virulence. However, only a minor fraction of sRNAs is well characterized with respect to the spectra of their targets, conditional expression profiles and actual mechanisms they use to regulate gene expression to control particular biological pathways. To learn more about the specific contribution of sRNAs to the global regulatory network controlling the Escherichia coli central carbon metabolism (CCM), we employed microarray analysis and compared transcriptome profiles of E. coli cells grown on two alternative minimal media supplemented with either pyruvate or glucose, respectively. Microarray analysis revealed that utilization of these alternative carbon sources led to profound differences in gene expression affecting all major gene clusters associated with CCM as well as expression of several known (CyaR, RyhB, GcvB and RyeA) and putative (C0652) sRNAs. To assess the impact of transcriptional reprogramming of gene expression on E. coli protein abundance, we also employed two-dimensional protein gel electrophoresis. Our experimental data made it possible to determine the major pathways for pyruvate assimilation when it is used as a sole carbon source and reveal the impact of other key processes (i.e., energy production, molecular transport and cell resistance to stress) associated with the CCM in E. coli. Moreover, some of these processes were apparently controlled by GcvB, RyhB and CyaR at the post-transcriptional level, thus indicating the complexity and interconnection of the regulatory networks that control CCM in bacteria.
    MeSH term(s) Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Gene Expression Regulation, Bacterial/genetics ; Glucose/metabolism ; Pyruvic Acid/metabolism ; RNA, Bacterial/genetics ; RNA, Small Untranslated/genetics ; Transcription, Genetic/genetics ; Transcriptome/genetics
    Chemical Substances Escherichia coli Proteins ; RNA, Bacterial ; RNA, Small Untranslated ; Pyruvic Acid (8558G7RUTR) ; Glucose (IY9XDZ35W2)
    Language English
    Publishing date 2019-07-30
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2044817-X
    ISSN 1617-4623 ; 1617-4615
    ISSN (online) 1617-4623
    ISSN 1617-4615
    DOI 10.1007/s00438-019-01597-1
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1198: Show issues Location:
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  10. Article ; Online: Metabolic remodeling in Escherichia coli MG1655. A prophage e14-encoded small RNA, co293, post-transcriptionally regulates transcription factors HcaR and FadR.

    Madikonda, Ashok Kumar / Shaikh, Akbarpasha / Khanra, Sonali / Yakkala, Harshita / Yellaboina, Sailu / Lin-Chao, Sue / Siddavattam, Dayananda

    The FEBS journal

    2020  Volume 287, Issue 21, Page(s) 4767–4782

    Abstract: In previous studies, we have shown the existence of metabolic remodeling in glucose-grown Escherichia coli MG1655 cells expressing the esterase Orf306 from the opd island of Sphingobium fuliginis. We now show that Orf306-dependent metabolic remodeling is ...

    Abstract In previous studies, we have shown the existence of metabolic remodeling in glucose-grown Escherichia coli MG1655 cells expressing the esterase Orf306 from the opd island of Sphingobium fuliginis. We now show that Orf306-dependent metabolic remodeling is due to regulation of a novel small RNA (sRNA). Endogenous propionate, produced due to the esterase/lipase activity of Orf306, repressed expression of a novel E. coli sRNA, co293. This sRNA post-transcriptionally regulates expression of the transcription factors HcaR and FadR either by inhibiting translation or by destabilizing their transcripts. Hence, repression of co293 expression elevates the levels of HcaR and FadR with consequent activation of alternative carbon catabolic pathways. HcaR activates the hca and MHP operons leading to upregulation of the phenyl propionate and hydroxy phenyl propionate (HPP) degradation pathways. Similarly, FadR stimulates the expression of the transcription factor IclR which negatively regulates the glyoxylate bypass pathway genes, aceBAK.
    MeSH term(s) Base Sequence ; Carbon/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli/virology ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Esterases/genetics ; Esterases/metabolism ; Gene Expression Regulation, Bacterial ; Metabolic Networks and Pathways/genetics ; Operon ; Prophages/genetics ; Prophages/metabolism ; RNA/genetics ; RNA/metabolism ; Sphingomonadaceae/genetics ; Sphingomonadaceae/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances Escherichia coli Proteins ; Transcription Factors ; RNA (63231-63-0) ; Carbon (7440-44-0) ; Esterases (EC 3.1.-)
    Language English
    Publishing date 2020-02-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2173655-8
    ISSN 1742-4658 ; 1742-464X
    ISSN (online) 1742-4658
    ISSN 1742-464X
    DOI 10.1111/febs.15247
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    Zs.A 260: Show issues Location:
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