Journal of Microbiology

Journal Article

Mutational analysis of the RNA helicase Dhh1 in Ste12 expression and yeast mating: Daehee Jung , Jihye Ahn , Boram Rhee , Jinmi Kim; J. Microbiol. 2017;55(5):373-378. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7020-4

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Dhh1 and Dhh1 homologues (RCK/p54/DDX6) are mem-bers of the DEAD-box protein family of RNA helicases. These proteins display conserved sequence motifs for ATPase and RNA binding activities. Dhh1 is a component of the P-bodies (processing bodies) of mRNA granules and functions as an mRNA decapping activator in Saccharomyces cerevisiae. Dhh1 also contributes to gene-specific regulation during yeast mating. The dhh1 deletion mutation results in a significant decrease in the expression of Ste12, a mating-specific trans-cription factor, showing severe mating defects. Here, we in-troduced amino-acid substitution mutations in the ATPase and RNA binding domains of Dhh1 and also constructed a deletion of 79 amino acids at the Q/P-rich C-terminal region. The mutations in ATPase A and B motif (K96R, D195A) and C-terminus deletion showed reduced levels of mating effi-ciency as well as Ste12 protein expression. The Q/P-rich C- terminal region of Dhh1 was dispensable for growth at non- permissive temperature 37°C but appeared to play an im-portant role in regulating the Ste12 protein expression and mating processes. The P-body accumulation induced by treatment with α-mating factor required ATPase, RNA-bind-ing and the Q/P-rich C-terminal domains of Dhh1.

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Fus3 and Tpk2 protein kinases regulate the phosphorylation-dependent functions of RNA helicase Dhh1 in yeast mating and Ste12 protein expression
Jaehee Hwang, Daehee Jung, Jinmi Kim
Journal of Microbiology.2022; 60(8): 843. CrossRef
The Role of DEAD-Box ATPases in Gene Expression and the Regulation of RNA–Protein Condensates
Karsten Weis, Maria Hondele
Annual Review of Biochemistry.2022; 91(1): 197. CrossRef
Roles of Dhh1 RNA helicase in yeast filamentous growth: Analysis of N-terminal phosphorylation residues and ATPase domains
Eunji Lee, Daehee Jung, Jinmi Kim
Journal of Microbiology.2020; 58(10): 853. CrossRef
Functional association of Loc1 and Puf6 with RNA helicase Dhh1 in translational regulation of Saccharomyces cerevisiae Ste12
Daehee Jung, Jong Seok Seo, Jayoung Nam, Jinmi Kim, Enrico Baruffini
PLOS ONE.2019; 14(7): e0220137. CrossRef
Roles of eIF4E-binding protein Caf20 in Ste12 translation and P-body formation in yeast
Kiyoung Park, Yu-Seon Lee, Daehee Jung, Jinmi Kim
Journal of Microbiology.2018; 56(10): 744. CrossRef

Research Support, Non-U.S. Gov'ts

Identification of Psk2, Skp1, and Tub4 as trans-acting factors for uORF-containing ROK1 mRNA in Saccharomyces cerevisiae: Soonmee Jeon , Suran Lim , Jeemin Ha , Jinmi Kim; J. Microbiol. 2015;53(9):616-622. Published online August 27, 2015; DOI: https://doi.org/10.1007/s12275-015-5389-5

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Abstract

Rok1, a DEAD-box RNA helicase, is involved in rRNA processing and the control of cell cycle progression in Saccharomyces cerevisiae. Rok1 protein expression is cell cycle-regulated, declining at G1/S and increasing at G2. The downregulation of Rok1 expression in G1/S phase is mediated by the inhibitory action of two upstream open reading frames (uORFs) in the ROK1 5􍿁-untranslated region (5􍿁UTR). We identified Psk2 (PAS kinase), Skp1 (kinetochore protein) and Tub4 (γ-tubulin protein) as ROK1 5􍿁UTR-interacting proteins using yeast three-hybrid system. A deletion analysis of PSK2 or inactivation of temperature-sensitive alleles of SKP1 and TUB4 revealed that Rok1 protein synthesis is repressed by Psk2 and Skp1. This repression appeared to be mediated through the ROK1 uORF1. In contrast, Tub4 plays a positive role in regulating Rok1 protein synthesis and likely after the uORF1-mediated inhibitory regulation. These results suggest that 5􍿁UTR-interacting proteins, identified using three hybrid screening, are important for uORF-mediated regulation of Rok1 protein expression.

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Identification of short open reading frames in plant genomes
Yong Feng, Mengyun Jiang, Weichang Yu, Jiannan Zhou
Frontiers in Plant Science.2023;[Epub] CrossRef
HST1 increases replicative lifespan of a sir2Δ mutant in the absence of PDE2 in Saccharomyces cerevisiae
Woo Kyu Kang, Mayur Devare, Jeong-Yoon Kim
Journal of Microbiology.2017; 55(2): 123. CrossRef

Hrq1 Facilitates Nucleotide Excision Repair of DNA Damage Induced by 4-Nitroquinoline-1-Oxide and Cisplatin in Saccharomyces cerevisiae: Do-Hee Choi , Moon-Hee Min , Min-Ji Kim , Rina Lee , Sung-Hun Kwon , Sung-Ho Bae; J. Microbiol. 2014;52(4):292-298. Published online March 29, 2014; DOI: https://doi.org/10.1007/s12275-014-4018-z

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Abstract

Hrq1 helicase is a novel member of the RecQ family. Among the five human RecQ helicases, Hrq1 is most homologous to RECQL4 and is conserved in fungal genomes. Recent genetic and biochemical studies have shown that it is a functional gene, involved in the maintenance of genome stability. To better define the roles of Hrq1 in yeast cells, we investigated genetic interactions between HRQ1 and several DNA repair genes. Based on DNA damage sensitivities induced by 4-nitroquinoline- 1-oxide (4-NQO) or cisplatin, RAD4 was found to be epistatic to HRQ1. On the other hand, mutant strains defective in either homologous recombination (HR) or postreplication repair (PRR) became more sensitive by additional deletion of HRQ1, indicating that HRQ1 functions in the RAD4-dependent nucleotide excision repair (NER) pathway independent of HR or PRR. In support of this, yeast twohybrid analysis showed that Hrq1 interacted with Rad4, which was enhanced by DNA damage. Overexpression of Hrq1K318A helicase-deficient protein rendered mutant cells more sensitive to 4-NQO and cisplatin, suggesting that helicase activity is required for the proper function of Hrq1 in NER.

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Metabolomics Combined with Physiology and Transcriptomics Reveal the Response of Samsoniella hepiali to Key Metabolic Pathways and Its Degradation Mechanism during Subculture
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Daria S. Spasskaya, Kirill A. Kulagin, Evgenia N. Grineva, Pamila J. Osipova, Svetlana V. Poddubko, Julia A. Bubis, Elizaveta M. Kazakova, Tomiris T. Kusainova, Vladimir A. Gorshkov, Frank Kjeldsen, Vadim L. Karpov, Irina A. Tarasova, Dmitry S. Karpov
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Hrq1/RECQL4 regulation is critical for preventing aberrant recombination during DNA intrastrand crosslink repair and is upregulated in breast cancer
Thong T. Luong, Zheqi Li, Nolan Priedigkeit, Phoebe S. Parker, Stefanie Böhm, Kyle Rapchak, Adrian V. Lee, Kara A. Bernstein, Dmitry A. Gordenin
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A skipping rope translocation mechanism in a widespread family of DNA repair helicases
Johann J Roske, Sunbin Liu, Bernhard Loll, Ursula Neu, Markus C Wahl
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Role and Regulation of the RECQL4 Family during Genomic Integrity Maintenance
Thong T. Luong, Kara A. Bernstein
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Zuo1 supports G4 structure formation and directs repair toward nucleotide excision repair
Alessio De Magis, Silvia Götz, Mona Hajikazemi, Enikő Fekete-Szücs, Marco Caterino, Stefan Juranek, Katrin Paeschke
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Ju-Hee Choi, Ye-Seul Lim, Min-Ku Kim, Sung-Ho Bae
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DNA Helicases as Safekeepers of Genome Stability in Plants
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The RecQ‐like helicase HRQ1 is involved in DNA crosslink repair in Arabidopsis in a common pathway with the Fanconi anemia‐associated nuclease FAN1 and the postreplicative repair ATPase RAD5A
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New Phytologist.2018; 218(4): 1478. CrossRef
Yeast Hrq1 shares structural and functional homology with the disease-linked human RecQ4 helicase
Cody M. Rogers, Joseph Che-Yen Wang, Hiroki Noguchi, Tsuyoshi Imasaki, Yuichiro Takagi, Matthew L. Bochman
Nucleic Acids Research.2017; 45(9): 5217. CrossRef
Interaction of RECQ4 and MCM10 is important for efficient DNA replication origin firing in human cells
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Oncotarget.2015; 6(38): 40464. CrossRef
DNA repair defects ascribed to pby1 are caused by disruption of Holliday junction resolvase Mus81-Mms4
Gizem Ölmezer, Dominique Klein, Ulrich Rass
DNA Repair.2015; 33: 17. CrossRef
Characterization of Hrq1-Rad14 Interaction in Saccharomyces cerevisiae
Moon-Hee Min, Min-Ji Kim, You-Jin Choi, Min-Ju You, Uy-Ra Kim, Hyo-Bin An, Chae-Hyun Kim, Chae-Yeon Kwon, Sung-Ho Bae
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Review

MINIREVIEW] To Peep into Pif1 Helicase: Multifaceted All the Way from Genome Stability to Repair-Associated DNA Synthesis: Woo-Hyun Chung; J. Microbiol. 2014;52(2):89-98. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3524-3

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Abstract

Pif1 DNA helicase is the prototypical member of a 5' to 3' helicase superfamily conserved from bacteria to humans. In Saccharomyces cerevisiae, Pif1 and its homologue Rrm3, localize in both mitochondria and nucleus playing multiple roles in the maintenance of genomic homeostasis. They display relatively weak processivities in vitro, but have largely non-overlapping functions on common genomic loci such as mitochondrial DNA, telomeric ends, and many replication forks especially at hard-to-replicate regions including ribosomal DNA and G-quadruplex structures. Recently, emerging evidence shows that Pif1, but not Rrm3, has a significant new role in repair-associated DNA synthesis with Polδ during homologous recombination stimulating D-loop migration for conservative DNA replication. Comparative genetic and biochemical studies on the structure and function of Pif1 family helicases across different biological systems are further needed to elucidate both diversity and specificity of their mechanisms of action that contribute to genome stability.

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The Pif1 helicase is actively inhibited during meiotic recombination which restrains gene conversion tract length
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Approaching Protein Barriers: Emerging Mechanisms of Replication Pausing in Eukaryotes
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Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition
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Onyekachi E. Ononye, Christopher W. Sausen, Lata Balakrishnan, Matthew L. Bochman
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Research Support, Non-U.S. Gov'ts

Hrq1 Functions Independently of Sgs1 to Preserve Genome Integrity in Saccharomyces cerevisiae: Do-Hee Choi , Rina Lee , Sung-Hun Kwon , Sung-Ho Bae; J. Microbiol. 2013;51(1):105-112. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-3048-2

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Abstract: Maintenance of genome stability in eukaryotes involves a number of conserved proteins, including RecQ helicases, which play multiple roles at various steps in homologous recombination and DNA repair pathways. Sgs1 has been described as the only RecQ helicase in lower eukaryotes. However, recent studies revealed the presence of a second RecQ helicase, Hrq1, which is most homologous to human RECQL4. Here we show that hrq1Δ mutation resulted in increased mitotic recombination and spontaneous mutation in Saccharomyces cerevisiae, and sgs1Δ mutation had additive effects on the phenotypes of hrq1Δ. We also observed that the hrq1Δ mutant was sensitive to 4-nitroquinoline 1-oxide and cisplatin, which was not complemented by overexpression of Sgs1. In addition, the hrq1Δ sgs1Δ double mutant displayed synthetic growth defect as well as a shortened chronological life span compared with the respective single mutants. Analysis of the type of age-dependent Canr mutations revealed that only point mutations were found in hrq1Δ, whereas significant numbers of gross deletion mutations were found in sgs1Δ. Our results suggest that Hrq1 is involved in recombination and DNA repair pathways in S. cerevisiae independent of Sgs1.

Kaposi’s Sarcoma-Associated Herpesvirus Viral Protein Kinase Interacts with RNA Helicase A and Regulates Host Gene Expression: Jae Eun Jong , Junsoo Park , Sunmi Kim , Taegun Seo; J. Microbiol. 2010;48(2):206-212. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-0021-1

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Abstract: RNA helicase A (RHA) containing the DExH motif is a human homolog of maleless protein that regulates expression of genes located in the Drosophila X chromosome during dosage compensation. RHA exerts helicase activity that unwinds double-stranded RNA and DNA to a single-strand form. The protein acts as a bridging factor mediating interactions of CBP/p300 and RNA pol II, and consequently affects gene expression. Kaposi’s sarcoma-associated herpesvirus (KSHV) is a member of the γ-herpesvirus subfamily that causes several disorders. The majority of herpesviruses commonly encode predicted viral protein kinases. KSHV open reading frame 36 (ORF36) codes for protein kinase domains, and functions as a serine/threonine protein kinase. KSHV ORF36 is classified as a late gene, as it is expressed during lytic replication and localized in the nuclei of KSHV-infected cells. Recent studies show that viral protein kinase (vPK) interacts with cellular proteins. In this study, we determined the cellular localization of vPK in KSHVinfected BCBL-1 cells using confocal microscopy. Proteomic analysis indicates that cellular proteins interacted with vPK, and co-immunoprecipitation reactions further reveal interactions between vPK and RHA. Moreover, KSHV vPK appeared to regulate the transcriptional activation of Cre promoter, and plays an important role in cellular transcription of RHA.

Reviews

REVIEW] The Linkage between Reverse Gyrase and Hyperthermophiles: A Review of Their Invariable Association: Michelle Heine , Sathees B.C. Chandra; J. Microbiol. 2009;47(3):229-234. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-009-0019-8

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Abstract: With the discovery of reverse gyrase in 1972, from Yellowstone National Park, isolated from Sulfolobus acidocaldarius, it has been speculated as to why reverse gyrase can be found in all hyperthermophiles and just what exactly its role is in hyperthermophilic organisms. Hyperthermophiles have been defined as organisms with an optimal growth temperature of above 85°C. Reverse gyrase is responsible for the introduction of positive supercoils into closed circular DNA. This review of reverse gyrase in hyperthermophilic microorganisms summarizes the last two decades of research performed on hyperthermophiles and reverse gyrase in an effort to provide an up to date synopsis of their invariable association. From the data gathered for this review it is reasonable to hypothesize that reverse gyrase is closely tied to hyperthermophilic life.

Rho-dependent Transcription Termination: More Questions than Answers: Sharmistha Banerjee , Jisha Chalissery , Irfan Bandey , Ranjan Sen; J. Microbiol. 2006;44(1):11-22.; DOI: https://doi.org/2342 [pii]

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Abstract: Escherichia coli protein Rho is required for the factor-dependent transcription termination by an RNA polymerase and is essential for the viability of the cell. It is a homohexameric protein that recognizes and binds preferably to C-rich sites in the transcribed RNA. Once bound to RNA, it utilizes RNA-dependent ATPase activity and subsequently ATPase-dependent helicase activity to unwind RNA-DNA hybrids and release RNA from a transcribing elongation complex. Studies over the past few decades have highlighted Rho as a molecule and have revealed much of its mechanistic properties. The recently solved crystal structure could explain many of its physiological functions in terms of its structure. Despite all these efforts, many of the fundamental questions pertaining to Rho recognition sites, differential ATPase activity in response to different RNAs, translocation of Rho along the nascent transcript, interactions with elongation complex and finally unwinding and release of RNA remain obscure. In the present review we have attempted to summarize ‘the knowns’ and ‘the unknowns’ of the Rho protein revealed by the recent developments in this field. An attempt has also been made to understand the physiology of Rho in the light of its phylogeny.

High Dosage of Rok1p, a Putative ATP-dependent RNA Helicase, Leads to a Cell Cycle Arrest at G1/S Stage in Saccharomyces cerevisiae: jeong, Hyun Sook , Oh, Jae Young , Kim, Jin Mi; J. Microbiol. 1998;36(2):139-144.

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Abstract: The ROK1 gene encodes a putative ATP-dependent RNA helicase which is essential for mitotic cell growth. ROK1 has been thought to affect microtubule and spindle pole body (SPB) functions in Saccharomyces cerevisiae. To investigate the intracellular functions of ROK1, we varied the Rok1 protein dosage in a cell and analyzed its phenotypic effects. Overexpression of the ROK1 gene by using a strong GAL1 promoter was lethal, leading cells to arrest at the unbudded stage. This arrest phenotype is very similar to that of the rok1 null mutation. Indirect immunofluorescence revealed that the majority of arrested cells contained a single SPB. Normas development of microtubules between the duplicated SPSs was rarely observed. Multinuclear cells with abnormal microtubule array were detected in small fraction. Taken together with the phenotype of the rlk1 null mutation, these results imply that ROK1 is required for cell cycle progression at the G1/S stage.

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