ORCID Profile
0000-0001-8950-793X
Current Organisation
Yokohama National University
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Publisher: American Society for Microbiology
Date: 02-09-2021
DOI: 10.1128/MRA.00478-21
Abstract: Enterobacter asburiae NCR1 is a plant growth-promoting rhizobacterium isolated from the rhizosphere of Carpobrotus rossii . We report the draft genome sequence of E. asburiae strain NCR1, which revealed many genes facilitating beneficial interactions with plant hosts.
Publisher: The Company of Biologists
Date: 2015
DOI: 10.1242/JCS.178830
Abstract: Current first-line artemisinin antimalarials are threatened by the emergence of resistant Plasmodium falciparum. Decreased sensitivity is evident in the initial (early ring) stage of intraerythrocytic development, making it critical to understand the action of artemisinins at this stage. We examined the roles of iron and haem in artemisinin activation in early rings using iron chelators and a specific haemoglobinase inhibitor (E64d). Quantitative modelling of the antagonism accounted for its complex dependence on chemical features of the artemisinins and on the drug exposure time, and showed that almost all artemisinin activity in early rings (& %) is due to haem-mediated activation. The surprising implication that haemoglobin uptake and digestion is active in early rings is supported by identification of active haemoglobinases (falcipains) at this stage. Genetic down-modulation of the expression of the two main cysteine protease haemoglobinases, falcipains 2 and 3, renders early ring stage parasites resistant to artemisinins. This confirms the important role of haemoglobin-degrading falcipains in artemisinin activation, and shows that changes in the rate of artemisinin activation could mediate high-level artemisinin resistance.
Publisher: Oxford University Press (OUP)
Date: 10-2022
DOI: 10.1111/LAM.13634
Abstract: Activated sludge bulking caused by filamentous bacteria is still a problem in wastewater treatment plants around the world. Bulking is a microbiological problem, and so its solution on species-specific basis is likely to be reached only after their ecology, physiology and metabolism is better understood. Culture-independent molecular methods have provided much useful information about this group of organisms, and in this review, the methods employed and the information they provide are critically assessed. Their application to understanding bulking caused by the most frequently seen filament in Japan, ‘Ca. Kouleothrix’, is used here as an ex le of how these techniques might be used to develop control strategies. Whole genome sequences are now available for some of filamentous bacteria responsible for bulking, and so it is possible to understand why these filaments might thrive in activated sludge plants, and provide clues as to how eventually they might be controlled specifically.
Publisher: American Society for Microbiology
Date: 31-08-2022
DOI: 10.1128/SPECTRUM.01524-22
Abstract: Pneumococcus is a pathogen of major public health importance. Current vaccines have limited valency, targeting a subset (up to 20) of the more than 100 capsule types (serotypes).
Publisher: Cold Spring Harbor Laboratory
Date: 14-04-2021
DOI: 10.1101/2021.04.14.439394
Abstract: Nonsense-mediated decay (NMD) is a conserved mRNA quality control process that eliminates transcripts bearing a premature termination codon. In addition to its role in removing erroneous transcripts, NMD is involved in post-transcriptional regulation of gene expression via programmed intron retention in metazoans. The apicomplexan parasite Plasmodium falciparum shows relatively high levels of intron retention, but it is unclear whether these variant transcripts are functional targets of NMD. In this study, we use CRISPR-Cas9 to disrupt and epitope-tag two core NMD components: Pf UPF1 (PF3D7_1005500) and Pf UPF2 (PF3D7_0925800). Using RNA-seq, we find that NMD in P. falciparum is highly derived and requires UPF2, but not UPF1 for transcript degradation. Furthermore, our work suggests that the majority of intron retention in P. falciparum has no functional role and that NMD is not required for parasite growth ex vivo . We localise both Pf UPF1 and Pf UPF2 to puncta within the parasite cytoplasm, which may represent processing bodies - ribonucleoparticles that are sites of cytoplasmic mRNA decay. Finally, we identify a number of mRNA-binding proteins that co-immunoprecipitate with the NMD core complex and propose a model for a ergent NMD that does not require Pf UPF1 and incorporates novel accessory proteins to elicit mRNA decay.
Publisher: Hindawi Limited
Date: 03-05-2016
DOI: 10.1111/CMI.12596
Abstract: The Plasmodium translocon for exported proteins (PTEX) has been established as the machinery responsible for the translocation of all classes of exported proteins beyond the parasitophorous vacuolar membrane of the intraerythrocytic malaria parasite. Protein export, particularly in the asexual blood stage, is crucial for parasite survival as exported proteins are involved in remodelling the host cell, an essential process for nutrient uptake, waste removal and immune evasion. Here, we have truncated the conserved C-terminus of one of the essential PTEX components, PTEX150, in Plasmodium falciparum in an attempt to create mutants of reduced functionality. Parasites tolerated C-terminal truncations of up to 125 amino acids with no reduction in growth, protein export or the establishment of new permeability pathways. Quantitative proteomic approaches however revealed a decrease in other PTEX subunits associating with PTEX150 in truncation mutants, suggesting a role for the C-terminus of PTEX150 in regulating PTEX stability. Our analyses also reveal three previously unreported PTEX-associated proteins, namely PV1, Pf113 and Hsp70-x (respective PlasmoDB numbers PF3D7_1129100, PF3D7_1420700 and PF3D7_0831700) and demonstrate that core PTEX proteins exist in various distinct multimeric forms outside the major complex.
Publisher: Frontiers Media SA
Date: 31-03-2021
DOI: 10.3389/FMICB.2021.650849
Abstract: Enterococcus faecalis is an opportunistic pathogen in the gut microbiota that’s associated with a range of difficult to treat nosocomial infections. It is also known to be associated with some colorectal cancers. Its resistance to a range of antibiotics and capacity to form biofilms increase its virulence. Unlike antibiotics, bacteriophages are capable of disrupting biofilms which are key in the pathogenesis of diseases such as UTIs and some cancers. In this study, bacteriophage EFA1, lytic against E. faecalis , was isolated and its genome fully sequenced and analyzed in silico . Electron microscopy images revealed EFA1 to be a Siphovirus . The bacteriophage was functionally assessed and shown to disrupt E. faecalis biofilms as well as modulate the growth stimulatory effects of E. faecalis in a HCT116 colon cancer cell co-culture system, possibly via the effects of ROS. The potential exists for further testing of bacteriophage EFA1 in these systems as well as in vivo models.
Publisher: Springer Science and Business Media LLC
Date: 29-04-2021
DOI: 10.1038/S41564-021-00892-1
Abstract: Many wastewater treatment plants around the world suffer from the operational problem of foaming. This is characterized by a persistent stable foam that forms on the aeration basin, which reduces effluent quality. The foam is often stabilized by a highly hydrophobic group of Actinobacteria known as the Mycolata
Publisher: MDPI AG
Date: 08-10-2020
DOI: 10.3390/V12101138
Abstract: Achromobacter spp. are becoming increasingly associated with lung infections in patients suffering from cystic fibrosis (CF). A. marplatensis, which is closely related to A. xylosoxidans, has been isolated from the lungs of CF patients and other human infections. This article describes the isolation, morphology and characterization of two lytic bacteriophages specific for an A. marplatensis strain isolated from a pneumonia patient. This host strain was the causal agent of hospital acquired pneumonia–the first clinical report of such an occurrence. Full genome sequencing revealed bacteriophage genomes ranging in size from 45901 to 46,328 bp. Transmission electron microscopy revealed that the two bacteriophages AMA1 and AMA2 belonged to the Siphoviridae family. Host range analysis showed that their host range did not extend to A. xylosoxidans. The possibility exists for future testing of such bacteriophages in the control of Achromobacter infections such as those seen in CF and other infections of the lungs. The incidence of antibiotic resistance in this genus highlights the importance of seeking adjuncts and alternatives in CF and other lung infections.
Publisher: MDPI AG
Date: 06-08-2021
DOI: 10.3390/V13081557
Abstract: Bacillus is a highly erse genus containing over 200 species that can be problematic in both industrial and medical settings. This is mainly attributed to Bacillus sp. being intrinsically resistant to an array of antimicrobial compounds, hence alternative treatment options are needed. In this study, two bacteriophages, PumA1 and PumA2 were isolated and characterized. Genome nucleotide analysis identified the two phages as novel at the DNA sequence level but contained proteins similar to phi29 and other related phages. Whole genome phylogenetic investigation of 34 phi29-like phages resulted in the formation of seven clusters that aligned with recent ICTV classifications. PumA1 and PumA2 share high genetic mosaicism and form a genus with another phage named WhyPhy, more recently isolated from the United States of America. The three phages within this cluster are the only candidates to infect B. pumilus. Sequence analysis of B. pumilus phage resistant mutants revealed that PumA1 and PumA2 require polymerized and peptidoglycan bound wall teichoic acid (WTA) for their infection. Bacteriophage classification is continuously evolving with the increasing phages’ sequences in public databases. Understanding phage evolution by utilizing a combination of phylogenetic approaches provides invaluable information as phages become legitimate alternatives in both human health and industrial processes.
Publisher: Springer Science and Business Media LLC
Date: 09-09-2014
DOI: 10.1007/S00726-014-1833-9
Abstract: Melittin (MLT) is a lytic peptide with a broad spectrum of activity against both eukaryotic and prokaryotic cells. To understand the role of proline and the thiol group of cysteine in the cytolytic activity of MLT, native MLT and cysteine-containing analogs were prepared using solid phase peptide synthesis. The antimicrobial and cytolytic activities of the monomeric and dimeric MLT peptides against different cells and model membranes were investigated. The results indicated that the proline residue was necessary for antimicrobial activity and cytotoxicity and its absence significantly reduced lysis of model membranes and hemolysis. Although lytic activity against model membranes decreased for the MLT dimer, hemolytic activity was increased. The native peptide and the MLT-P14C monomer were mainly unstructured in buffer while the dimer adopted a helical conformation. In the presence of neutral and negatively charged vesicles, the helical content of the three peptides was significantly increased. The lytic activity, therefore, is not correlated to the secondary structure of the peptides and, more particularly, on the propensity to adopt helical conformation.
Publisher: American Society for Microbiology
Date: 28-04-2020
Abstract: The trafficking of the virulence antigen Pf EMP1 and its presentation at the knob structures at the surface of parasite-infected RBCs are central to severe adhesion-related pathologies such as cerebral and placental malaria. This work adds to our understanding of how PfEMP1 is trafficked to the RBC membrane by defining the protein-protein interaction networks that function at the Maurer’s clefts controlling PfEMP1 loading and unloading. We characterize a protein needed for virulence protein trafficking and provide new insights into the mechanisms for host cell remodeling, parasite survival within the host, and virulence.
Publisher: Springer Science and Business Media LLC
Date: 10-07-2017
DOI: 10.1038/NCOMMS16044
Abstract: The malaria parasite, Plasmodium falciparum , displays the P. falciparum erythrocyte membrane protein 1 ( Pf EMP1) on the surface of infected red blood cells (RBCs). We here examine the physical organization of Pf EMP1 trafficking intermediates in infected RBCs and determine interacting partners using an epitope-tagged minimal construct ( Pf EMP1B). We show that parasitophorous vacuole (PV)-located Pf EMP1B interacts with components of the PTEX ( Plasmodium Translocon of EXported proteins) as well as a novel protein complex, EPIC (Exported Protein-Interacting Complex). Within the RBC cytoplasm Pf EMP1B interacts with components of the Maurer’s clefts and the RBC chaperonin complex. We define the EPIC interactome and, using an inducible knockdown approach, show that depletion of one of its components, the parasitophorous vacuolar protein-1 (PV1), results in altered knob morphology, reduced cell rigidity and decreased binding to CD36. Accordingly, we show that deletion of the P lasmodium berghei homologue of PV1 is associated with attenuation of parasite virulence in vivo .
Publisher: Public Library of Science (PLoS)
Date: 06-10-2017
Publisher: MDPI AG
Date: 11-02-2023
DOI: 10.3390/V15020506
Abstract: Bacteriophages, viruses that infect bacteria, are currently receiving significant attention amid an ever-growing global antibiotic resistance crisis. In tandem, a surge in the availability and affordability of next-generation and third-generation sequencing technologies has driven the deposition of a wealth of phage sequence data. Here, we have isolated a novel Escherichia phage, YF01, from a municipal wastewater treatment plant in Yokohama, Japan. We demonstrate that the YF01 phage shares a high similarity to a collection of thirty-five Escherichia and Shigella phages found in public databases, six of which have been previously classified into the Kuravirus genus by the International Committee on Taxonomy of Viruses (ICTV). Using modern phylogenetic approaches, we demonstrate that an expansion and reshaping of the current six-membered Kuravirus genus is required to accommodate all thirty-six member phages. Ultimately, we propose the creation of three additional genera, Vellorevirus, Jinjuvirus, and Yesanvirus, which will allow a more organized approach to the addition of future Kuravirus-like phages.
Publisher: Springer Science and Business Media LLC
Date: 28-11-2022
DOI: 10.1186/S12864-022-09023-4
Abstract: Bacteriophages are widely considered to be highly abundant and genetically erse, with their role in the evolution and virulence of many pathogens becoming increasingly clear. Less attention has been paid on phages preying on Bacillus , despite the potential for some of its members, such as Bacillus anthracis , to cause serious human disease. We have isolated five phages infecting the causative agent of anthrax, Bacillus anthracis . Using modern phylogenetic approaches we place these five new Bacillus phages, as well as 21 similar phage genomes retrieved from publicly available databases and metagenomic datasets into the Tyrovirus group, a newly proposed group named so due to the conservation of three distinct tyrosine recombinases. Genomic analysis of these large phages (~ 160–170 kb) reveals their DNA packaging mechanism and genomic features contributing to virion morphogenesis, host cell lysis and phage DNA replication processes. Analysis of the three tyrosine recombinases suggest Tyroviruses undergo a prophage lifecycle that may involve both host integration and plasmid stages. Further we show that Tyroviruses rely on ergent invasion mechanisms, with a subset requiring host S-layer for infection. Ultimately, we expand upon our understanding on the classification, phylogeny, and genomic organisation of a new and substantial phage group that prey on critically relevant Bacillus species. In an era characterised by a rapidly evolving landscape of phage genomics the deposition of future Tyroviruses will allow the further unravelling of the global spread and evolutionary history of these Bacillus phages.
Publisher: Hindawi Limited
Date: 14-03-2013
DOI: 10.1111/CMI.12125
Publisher: Elsevier BV
Date: 2020
Publisher: Oxford University Press (OUP)
Date: 10-2022
DOI: 10.1111/LAM.13742
Abstract: The production of a stable foam on the surfaces of reactors is a global operating problem in activated sludge plants. In many cases, these foams are stabilized by hydrophobic members of the Mycolata, a group of Actinobacteria whose outer membranes contain long-chain hydroxylated mycolic acids. There is currently no single strategy which works for all foams. One attractive approach is to use lytic bacteriophages specific for the foam stabilizing Mycolata population. Such phages are present in activated sludge mixed liquor and can be recovered readily from it. However, no phage has been recovered which lyses Gordonia amarae and Gordonia pseudoamarae, probably the most common foaming Mycolata members. Whole genome sequencing revealed that both G. amarae and G. pseudoamarae from plants around the world are particularly well endowed with genes encoding antiviral defence mechanisms. However, both these populations were lysed rapidly by a parasitic nanobacterium isolated from a plant in Australia. This organism, a member of the Saccharibacteria, was also effective against many other Mycolata, thus providing a potential agent for control of foams stabilized by them.
Publisher: American Society for Microbiology
Date: 26-08-2021
DOI: 10.1128/MRA.00487-21
Abstract: Enterobacter mori is an important plant pathogen. Here, we report the draft genome sequence of the plant-associated strain Enterobacter mori NSE2, which was found to harbor genes for promotive and pathogenic interactions with plants.
Publisher: Microbiology Society
Date: 18-10-2022
Abstract: The taxonomic status of two Gordonia strains, designated BEN371 and CON9 T , isolated from stable foams on activated sludge plants was the subject of a polyphasic study which also included the type strains of Gordonia species and three authenticated Gordonia amarae strains recovered from such foams. Phylogenetic analyses of 16S rRNA gene sequences showed that these isolates formed a compact cluster suggesting a well-supported lineage together with a second branch containing the G. amarae strains. A phylogenomic tree based on sequences of 92 core genes extracted from whole genome sequences of the isolates, the G. amarae strains and Gordonia type strains confirmed the assignment of the isolates and the G. amarae strains to separate but closely associated lineages. Average nucleotide index (ANI) and digital DNA–DNA hybridisation (dDDH) similarities showed that BEN371 and CON9 T belonged to the same species and had chemotaxonomic and morphological features consistent with their assignment to the genus Gordonia . The isolates and the G. amarae strains were distinguished using a range of phenotypic features and by low ANI and dDDH values of 84.2 and 27.0 %, respectively. These data supplemented with associated genome characteristics show that BEN371 and CON9 T represent a novel species of the genus Gordonia . The name proposed for members of this taxon is Gordonia pseudamarae sp. nov. with isolate CON9 T (=DSM 43602 T =JCM 35249 T ) as the type strain.
Publisher: Public Library of Science (PLoS)
Date: 07-09-2021
DOI: 10.1371/JOURNAL.PONE.0257102
Abstract: The bacterial genus Klebsiella includes the closely related species K . michiganensis , K . oxytoca and K . pneumoniae , which are capable of causing severe disease in humans. In this report we describe the isolation, genomic and functional characterisation of the lytic bacteriophage KMI8 specific for K . michiganensis . KMI8 belongs to the family Drexlerviridae , and has a novel genome which shares very little homology (71.89% identity over a query cover of only 8%) with that of its closest related bacteriophages (Klebsiella bacteriophage LF20 (MW417503.1) Klebsiella bacteriophage 066039 (MW042802.1). KMI8, which possess a putative endosialidase (depolymerase) enzyme, was shown to be capable of degrading mono-biofilms of a strain of K . michiganensis that carried the polysaccharide capsule KL70 locus. This is the first report of a lytic bacteriophage for K . michiganensis , which is capable of breaking down a biofilm of this species.
Publisher: MDPI AG
Date: 12-07-2019
Abstract: Bacteriophages (phages) are biological entities that have attracted a great deal of attention in recent years. They have been reported as the most abundant biological entities on the planet and their ability to impact the composition of bacterial communities is of great interest. In this review, we aim to explore where phages exist in natural and artificial environments and how they impact communities. The natural environment in this review will focus on the human body, soils, and the marine environment. In these naturally occurring environments there is an abundance of phages suggesting a role in the maintenance of bacterial community homeostasis. The artificial environment focuses on wastewater treatment plants, industrial processes, followed by pharmaceutical formulations. As in natural environments, the existence of bacteria in manmade wastewater treatment plants and industrial processes inevitably attracts phages. The presence of phages in these environments can inhibit the bacteria required for efficient water treatment or food production. Alternatively, they can have a positive impact by eliminating recalcitrant organisms. Finally, we conclude by describing how phages can be manipulated or formulated into pharmaceutical products in the laboratory for use in natural or artificial environments.
Publisher: Wiley
Date: 25-09-2015
DOI: 10.1111/MMI.13201
Publisher: American Society for Microbiology
Date: 15-06-2023
DOI: 10.1128/SPECTRUM.05332-22
Abstract: Amid the global antibiotic resistance crisis, novel antimicrobials are needed to treat problematic bacterial infections, including those from the Burkholderia cepacia complex. One such alternative is the use of bacteriophages however, a lot is still unknown about their biology.
Publisher: Springer Science and Business Media LLC
Date: 24-01-2022
DOI: 10.1186/S40168-021-01203-W
Abstract: Understanding how elevated atmospheric CO 2 (eCO 2 ) impacts on phosphorus (P) transformation in plant rhizosphere is critical for maintaining ecological sustainability in response to climate change, especially in agricultural systems where soil P availability is low. This study used rhizoboxes to physically separate rhizosphere regions (plant root-soil interface) into 1.5-mm segments. Wheat plants were grown in rhizoboxes under eCO 2 (800 ppm) and ambient CO 2 (400 ppm) in two farming soils, Chromosol and Vertosol, supplemented with phytate (organic P). Photosynthetic carbon flow in the plant-soil continuum was traced with 13 CO 2 labeling. Amplicon sequencing was performed on the rhizosphere-associated microbial community in the root-growth zone, and 1.5 mm and 3 mm away from the root. Elevated CO 2 accelerated the mineralization of phytate in the rhizosphere zones, which corresponded with increases in plant-derived 13 C enrichment and the relative abundances of discreet phylogenetic clades containing Bacteroidetes and Gemmatimonadetes in the bacterial community, and Funneliformis affiliated to arbuscular mycorrhizas in the fungal community. Although the licon sequence variants (ASVs) associated the stimulation of phytate mineralization under eCO 2 differed between the two soils, these ASVs belonged to the same phyla associated with phytase and phosphatase production. The symbiotic mycorrhizas in the rhizosphere of wheat under eCO 2 benefited from increased plant C supply and increased P access from soil. Further supportive evidence was the eCO 2 -induced increase in the genetic pool expressing the pentose phosphate pathway, which is the central pathway for biosynthesis of RNA/DNA precursors. The results suggested that an increased belowground carbon flow under eCO 2 stimulated bacterial growth, changing community composition in favor of phylotypes capable of degrading aromatic P compounds. It is proposed that energy investments by bacteria into anabolic processes increase under eCO 2 to level microbial P-use efficiencies and that synergies with symbiotic mycorrhizas further enhance the competition for and mineralization of organic P.
Publisher: Springer Science and Business Media LLC
Date: 25-09-2020
Publisher: American Society for Microbiology
Date: 09-04-2020
DOI: 10.1128/MRA.00030-20
Abstract: We report the complete genome sequence of Moraxella osloensis strain YV1, which was isolated from a wastewater treatment plant in Australia. The YV1 genome comprises a 2,615,801-bp chromosome and four plasmids. Moraxella osloensis strain YV1 displays the distinctive morphology of Eikelboom morphotype 1863.
No related grants have been discovered for Steven Batinovic.