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  1. AU="Gribchenko, Emma S"
  2. AU="Ge, Xiangyang"
  3. AU="Das, Arindam"
  4. AU="Taus, Naomi S"
  5. AU="Kayagaki, Nobuhiko"
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  1. Article ; Online: Draft Genome Sequence of Rhizobium ruizarguesonis (Rhizobium leguminosarum) Strain 1TK341.

    Afonin, Alexey M / Gribchenko, Emma S / Sulima, Anton S / Akhtemova, Gulnar A / Zhukov, Vladimir A

    Microbiology resource announcements

    2022  Volume 11, Issue 4, Page(s) e0102321

    Abstract: Rhizobium ruizarguesonis (Rhizobium leguminosarum) strain 1TK341 was isolated from pink nodules of fixation-negative mutant line P61 of pea (Pisum sativum L.) grown in soil. Here, we report the draft genome sequence of the strain. ...

    Abstract Rhizobium ruizarguesonis (Rhizobium leguminosarum) strain 1TK341 was isolated from pink nodules of fixation-negative mutant line P61 of pea (Pisum sativum L.) grown in soil. Here, we report the draft genome sequence of the strain.
    Language English
    Publishing date 2022-03-17
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.01023-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Complete Genome Sequence of an Efficient Rhizobium leguminosarum bv. viciae Strain, A1.

    Afonin, Alexey M / Gribchenko, Emma S / Sulima, Anton S / Zhukov, Vladimir A

    Microbiology resource announcements

    2020  Volume 9, Issue 19

    Abstract: Rhizobium ... ...

    Abstract Rhizobium leguminosarum
    Language English
    Publishing date 2020-05-07
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00249-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: DNA Methylation Patterns Differ between Free-Living

    Afonin, Alexey M / Gribchenko, Emma S / Zorin, Evgeny A / Sulima, Anton S / Zhukov, Vladimir A

    Microorganisms

    2021  Volume 9, Issue 12

    Abstract: Rhizobium ... ...

    Abstract Rhizobium leguminosarum
    Language English
    Publishing date 2021-11-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms9122458
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: DNA Methylation Patterns Differ between Free-Living Rhizobium leguminosarum RCAM1026 and Bacteroids Formed in Symbiosis with Pea (Pisum sativum L.)

    Afonin, Alexey M. / Gribchenko, Emma S. / Zorin, Evgeny A. / Sulima, Anton S. / Zhukov, Vladimir A.

    Microorganisms. 2021 Nov. 28, v. 9, no. 12

    2021  

    Abstract: Rhizobium leguminosarum (Rl) is a common name for several genospecies of rhizobia able to form nitrogen-fixing nodules on the roots of pea (Pisum sativum L.) while undergoing terminal differentiation into a symbiotic form called bacteroids. In this work, ...

    Abstract Rhizobium leguminosarum (Rl) is a common name for several genospecies of rhizobia able to form nitrogen-fixing nodules on the roots of pea (Pisum sativum L.) while undergoing terminal differentiation into a symbiotic form called bacteroids. In this work, we used Oxford Nanopore sequencing to analyze the genome methylation states of the free-living and differentiated forms of the Rl strain RCAM1026. The complete genome was assembled; no significant genome rearrangements between the cell forms were observed, but the relative abundances of replicons were different. GANTC, GGCGCC, and GATC methylated motifs were found in the genome, along with genes encoding methyltransferases with matching predicted target motifs. The GGCGCC motif was completely methylated in both states, with two restriction–modification clusters on different replicons enforcing this specific pattern of methylation. Methylation patterns for the GANTC and GATC motifs differed significantly depending on the cell state, which indicates their possible connection to the regulation of symbiotic differentiation. Further investigation into the differences of methylation patterns in the bacterial genomes coupled with gene expression analysis is needed to elucidate the function of bacterial epigenetic regulation in nitrogen-fixing symbiosis.
    Keywords DNA methylation ; Pisum sativum ; Rhizobium leguminosarum ; common names ; epigenetics ; gene expression ; methyltransferases ; nanopores ; nitrogen fixation ; peas ; symbiosis
    Language English
    Dates of publication 2021-1128
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms9122458
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: The Succession of the Cellulolytic Microbial Community from the Soil during Oat Straw Decomposition.

    Kimeklis, Anastasiia K / Gladkov, Grigory V / Orlova, Olga V / Afonin, Alexey M / Gribchenko, Emma S / Aksenova, Tatiana S / Kichko, Arina A / Pinaev, Alexander G / Andronov, Evgeny E

    International journal of molecular sciences

    2023  Volume 24, Issue 7

    Abstract: The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil ... ...

    Abstract The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.
    MeSH term(s) Soil/chemistry ; Avena ; Microbiota ; Bacteria/genetics ; Bacteria/metabolism ; Ascomycota ; Glycoside Hydrolases/metabolism ; Soil Microbiology
    Chemical Substances Soil ; Glycoside Hydrolases (EC 3.2.1.-)
    Language English
    Publishing date 2023-03-28
    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/ijms24076342
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) Roots

    Zorin, Evgeny A / Afonin, Alexey M / Kulaeva, Olga A / Gribchenko, Emma S / Shtark, Oksana Y / Zhukov, Vladimir A

    Plants. 2020 Dec. 03, v. 9, no. 12

    2020  

    Abstract: Alternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with ... ...

    Abstract Alternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with soil microorganisms is not fully understood. In this work, a comprehensive analysis of the transcriptome of garden pea (Pisum sativum L.) roots in symbiosis with arbuscular mycorrhiza was performed using RNAseq and following bioinformatic analysis. AS profiles of mycorrhizal and control roots were highly similar, intron retention accounting for a large proportion of the observed AS types (67%). Using three different tools (SUPPA2, DRIMSeq and IsoformSwitchAnalyzeR), eight genes with AS events specific for mycorrhizal roots of pea were identified, among which four were annotated as encoding an apoptosis inhibitor protein, a serine/threonine-protein kinase, a dehydrodolichyl diphosphate synthase, and a pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1. In pea mycorrhizal roots, the isoforms of these four genes with preliminary stop codons leading to a truncated ORFs were up-regulated. Interestingly, two of these four genes demonstrating mycorrhiza-specific AS are related to the process of splicing, thus forming parts of the feedback loops involved in fine-tuning of gene expression during mycorrhization.
    Keywords Pisum sativum subsp. sativum var. sativum ; RNA helicases ; Rhizophagus irregularis ; accounting ; alternative splicing ; apoptosis ; bioinformatics ; gene expression ; introns ; mycorrhizal fungi ; peas ; roots ; stop codon ; transcriptome ; transcriptomics ; vesicular arbuscular mycorrhizae
    Language English
    Dates of publication 2020-1203
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    Note NAL-light
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants9121700
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Complete Genome Sequence of the Bacterial Component of Mysorin Biopreparation.

    Afonin, Alexey M / Gribchenko, Emma S / Akhtemova, Gulnar A / Laktionov, Yuri V / Kozhemyakov, Andrej P / Zhukov, Vladimir A

    Microbiology resource announcements

    2021  Volume 10, Issue 11

    Abstract: Plants can form various beneficial associations with soil microorganisms, such as associations with plant growth-promoting bacteria (PGPB). In this work, we report the full-genome sequence of the component of Mysorin biopreparation, identified ... ...

    Abstract Plants can form various beneficial associations with soil microorganisms, such as associations with plant growth-promoting bacteria (PGPB). In this work, we report the full-genome sequence of the component of Mysorin biopreparation, identified as
    Language English
    Publishing date 2021-03-18
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.01287-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Complete Genome Sequence of Sinorhizobium meliloti S35m, a Salt-Tolerant Isolate from Alfalfa Rhizosphere in Soil Native to the Caucasus Region.

    Muntyan, Victoria S / Afonin, Alexey M / Vladimirova, Maria E / Saksaganskaya, Alla S / Gribchenko, Emma S / Baturina, Olga / Roumiantseva, Marina L

    Microbiology resource announcements

    2021  Volume 10, Issue 11

    Abstract: The genome of a symbiotically effective salt-tolerant strain, ...

    Abstract The genome of a symbiotically effective salt-tolerant strain,
    Language English
    Publishing date 2021-03-18
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.01417-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Inter-library loan at ZB MED

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  9. Article: Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (

    Zorin, Evgeny A / Afonin, Alexey M / Kulaeva, Olga A / Gribchenko, Emma S / Shtark, Oksana Y / Zhukov, Vladimir A

    Plants (Basel, Switzerland)

    2020  Volume 9, Issue 12

    Abstract: Alternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with ... ...

    Abstract Alternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with soil microorganisms is not fully understood. In this work, a comprehensive analysis of the transcriptome of garden pea (
    Language English
    Publishing date 2020-12-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants9121700
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: A variable gene family encoding nodule-specific cysteine-rich peptides in pea (

    Zorin, Evgeny A / Kliukova, Marina S / Afonin, Alexey M / Gribchenko, Emma S / Gordon, Mikhail L / Sulima, Anton S / Zhernakov, Aleksandr I / Kulaeva, Olga A / Romanyuk, Daria A / Kusakin, Pyotr G / Tsyganova, Anna V / Tsyganov, Viktor E / Tikhonovich, Igor A / Zhukov, Vladimir A

    Frontiers in plant science

    2022  Volume 13, Page(s) 884726

    Abstract: Various legume plants form root nodules in which symbiotic bacteria (rhizobia) fix atmospheric nitrogen after differentiation into a symbiotic form named bacteroids. In some legume species, bacteroid differentiation is promoted by defensin-like nodule- ... ...

    Abstract Various legume plants form root nodules in which symbiotic bacteria (rhizobia) fix atmospheric nitrogen after differentiation into a symbiotic form named bacteroids. In some legume species, bacteroid differentiation is promoted by defensin-like nodule-specific cysteine-rich (NCR) peptides. NCR peptides have best been studied in the model legume
    Language English
    Publishing date 2022-09-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2022.884726
    Database MEDical Literature Analysis and Retrieval System OnLINE

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