Journal of Microbiology

Volume 47(3); June 2009

Review

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.

Research Support, Non-U.S. Gov't

Microbial Diversity of a Sulfide Black Smoker in Main Endeavour Hydrothermal Vent Field, Juan de Fuca Ridge: Huaiyang Zhou , Jiangtao Li , Xiaotong Peng , Jun Meng , Fengping Wang , Yuncan Ai; J. Microbiol. 2009;47(3):235-247. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0311-z

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Abstract

Submarine hydrothermal vents are among the least-understood habitats on Earth but have been the intense focus of research in the past 30 years. An active hydrothermal sulfide chimney collected from the Dudley site in the Main Endeavour vent Field (MEF) of Juan de Fuca Ridge was investigated using mineralogical and molecular approaches. Mineral analysis indicated that the chimney was composed mainly of Fe-, Zn- and Cu-rich sulfides. According to phylogenetic analysis, within the Crenarchaeota, clones of the order Desulfurococcales predominated, comprising nearly 50% of archaeal clones. Euryarchaeota were composed mainly of clones belonging to Thermococcales and deep-sea hydrothermal vent Euryarchaeota (DHVE), each of which accounted for about 20% of all clones. Thermophilic or hyperthermophilic physiologies were common to the predominant archaeal groups. More than half of bacterial clones belonged to ε-Proteobacteria, which confirmed their prevalence in hydrothermal vent environments. Clones of Proteobacteria (γ-, δ-, β-), Cytophaga-Flavobacterium-Bacteroides (CFB) and Deinococcus-Thermus occurred as well. It was remarkable that methanogens and methanotrophs were not detected in our 16S rRNA gene library. Our results indicated that sulfur-related metabolism, which included sulfur-reducing activity carried out by thermophilic archaea and sulfur-oxidizing by mesophilic bacteria, was common and crucial to the vent ecosystem in Dudley hydrothermal site.

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Journal Article

Nematicidal Activity of Paecilomyces spp. and Isolation of a Novel Active Compound: Ya-Jun Liu , Chong-Yan Zhai , Yi Liu , Ke-Qin Zhang; J. Microbiol. 2009;47(3):248-252. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-009-0012-2

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Abstract

Many species of Paecilomyces are entomogenous fungi and several are efficacious toward nematodes. To study the potential of Paecilomyces species in controlling nematodes, fungal extracts of 40 Paecilomyces spp. were evaluated for their nematicidal activity against Bursaphelenchus xylophilus and Panagrellus redivivus. The extracts of six Paecilomyces spp. exhibited the nematicidal activity against P. redivivus, and 11 species exhibited the nematicidal activity against B. xylophilus. The methanol extract of strain 1.01761 incubating on Czapek solid medium killed more than 95% P. redivivus in 24 h at 5 mg/ml, and the filtrate of strain 1.01788 cultured in Sabouraud''s broth medium resulted in 90% mortality of B. xylophilus in 24 h at 5 mg/ml. A novel nematicidal compound, 4-(4’-carboxy-2’-ethyl-hydroxypentyl)-5,6-dihydro-6-methylcyclobuta[b]pyridine-3,6-dicarboxylic acid, was isolated from Paecilomyces sp. YMF1.01761. The LD50 value of the compound within 24 h against P. redivivus was 50.86 mg/L, against Meloidogyne incognita was 47.1 mg/L, and against B. xylophilus was 167.7 mg/L.

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Secondary Metabolites and Their Bioactivities Produced by Paecilomyces
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Research Support, Non-U.S. Gov'ts

Evaluation of Three Molecular Methods of Repetitive Element Loci for Differentiation of Mycobacterium avium subsp. paratuberculosis (MAP): Amr El-Sayed , Abdulwahed Ahmed Hassan , Saleh Natour , Amir Abdulmawjood , Michael Bulte , Wilfried Wolter , Michael Zschock; J. Microbiol. 2009;47(3):253-259. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0257-1

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Abstract

The aim of the present study is to evaluate the efficiency of three methods to determine the molecular diversity of 34 Mycobacterium avium subsp. paratuberculosis (MAP) strains isolated from 17 cattle herds. The applied methods included the analysis of sequence polymorphism of the mononucleotide (G1 and G2) and trinucleotide sequences (GGT) of the Short Sequence Repeats (SSR) and the determination of size polymorphism of 9 different Mycobacterial Interspersed Repetitive Units (MIRU) and 6 Variable Number Tandem Repeats (VNTR). Sequence analysis of SSR of 34 isolates showed 4, 6, and 2 alleles of G1, G2, and GGT repeats, respectively. The amplification of the investigated 9 MIRU units revealed only two discriminatory genotyping systems (MIRU2 and MIRU3). Out of 6 VNTR PCR differentiation methods, only one method could be recommended for genotyping purposes. The profile 7g-12g-4ggt-II-b-2 of the combination systems G1-G2-GGT-MIRU2-MIRU3-VNTR1658 dominates among the examined isolates and was
detected in 14.7% of the isolates. The use of certain repetitive loci of SSR, MIRU, and VNTR techniques in this study showed greater potential than others for the characterization of MAP isolates. The recommended loci can be used for the epidemiological tracing of MAP field strains and to determine the relationships
between isolates in different herds.

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Genotyping methods and molecular epidemiology ofMycobacterium aviumsubsp.paratuberculosis(MAP)
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Typing of Mycobacterium avium Subspecies paratuberculosis Isolates from Newfoundland Using Fragment Analysis
Milka P. Podder, Susan E. Banfield, Greg P. Keefe, Hugh G. Whitney, Kapil Tahlan, Igor Mokrousov
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G. S. Abdellrazeq, M. M. El-Naggar, S. A. Khaliel, A. E. Gamal-Eldin
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Molecular characterization ofMycobacterium aviumsubsp.paratuberculosisfield isolates recovered from dairy cattle in Germany
Mohamed Salem, Saleh Natur, Amr A. El-Sayed, Abdulwahed Hassan, Georg Baljer, Michael Zschöck
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Mycobacterium avium subspecies paratuberculosis: an insidious problem for the ruminant industry
Mohamed Salem, Carsten Heydel, Amr El-Sayed, Samia A. Ahmed, Michael Zschöck, George Baljer
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The Three-Dimensional Morphology of Candida albicans as Seen by High-Resolution Scanning Electron Microscopy: Michela Isola , Raffaella Isola , Maria Serenella Lantini , Alessandro Riva; J. Microbiol. 2009;47(3):260-264. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0212-1

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Abstract

The fine structure of Candida albicans has been repeatedly described by transmission electron microscopy, whereas studies by high-resolution scanning electron microscopy (HRSEM) are rare and devoted solely to the study of its external morphology. This report describes the results of an HRSEM study on C. albicans carried out by an osmium maceration protocol modified to better retain the structural characteristics of this yeast. Thus, we visualized various intracellular structures including invaginations of cell membrane (plasmalemmasomes), nuclear envelope, mitochondria, the vacuolar system, and two additional structures that might represent a form of endoplasmic reticulum and the Golgi apparatus. The present investigation, which for the first time shows the organelles of C. albicans at the 3D level, may lead to a better understanding of its cell physiology.

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A New Dactylella Species from Orbilia alba: ZeFen Yu , YanJie Kong , Ying Zhang , Min Qiao , JianWei Guo , Ke-Qin Zhang; J. Microbiol. 2009;47(3):265-269. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0301-1

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Abstract

A new Dactylella species, Dactylella alba was isolated from the ascospores of Orbilia alba collected in Wen- shan County, Yunnan Province, China. Conidiophores were either not branched or occasionally branched, bearing divergent sterigmata on the tip with single conidium on each. Conidia were elongated ellipsoids, 1-2 septate, mostly 1 septate. By combining the ITS sequence with morphological characteristics, a new anamorphic species is described and illustrated together with its teleomorph.

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Effect of Glycosylation on the Biochemical Properties of beta-Xylosidases from Aspergillus versicolor: Alexandre Favarin Somera , Marita Gimenez Pereira , Luis Henrique Souza Guimaraes , Maria de Lourdes Teixeira de Moraes Polizeli , Hector Francisco Terenzi , Rosa Prazeres Melo Furriel , Joao Atilio Jorge; J. Microbiol. 2009;47(3):270-276. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0286-9

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Abstract

Aspergillus versicolor grown on xylan or xylose produces two beta-xylosidases with differences in biochemical properties and degree of glycosylation. We investigated the alterations in the biochemical properties of these beta-xylosidases after deglycosylation with Endo-H or PNGase F. After deglycosylation, both enzymes migrated faster in PAGE or SDS-PAGE exhibiting the same Rf. Temperature optimum of xylan-induced and xylose-induced beta-xylosidases was 45oC and 40oC, respectively, and 35oC after deglycosylation. The xylan- induced enzyme was more active at acidic pH. After deglycosylation, both enzymes had the same pH optimum of 6.0. Thermal resistance at 55oC showed half-life of 15 min and 9 min for xylose- and xylan-induced enzymes, respectively. After deglycosylation, both enzymes exhibited half-lives of 7.5 min. Native enzymes exhibited different responses to ions, while deglycosylated enzymes exhibited identical responses. Limited proteolysis yielded similar polypeptide profiles for the deglycosylated enzymes, suggesting a common polypeptide core with differential glycosylation apparently responsible for their biochemical and biophysical differences.

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Molecular Analysis of the Copper-Responsive CopRSCD of a Pathogenic Pseudomonas fluorescens Strain: Yong-hua Hu , Hua-lei Wang , Min Zhang , Li Sun; J. Microbiol. 2009;47(3):277-286. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0278-9

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Abstract

CopRS/CopABCD is one of the known systems that control copper homeostasis in bacteria. Although CopRS/CopABCD homologues are found to exist in Pseudomonas fluorescens, the potential role of this system in P. fluorescens has not been investigated. In this study a genetic cluster, consisting of copR, S, C, and D but lacking copAB, was identified in a pathogenic P. fluorescens strain (TSS) isolated from diseased fish. The copRSCD cluster was demonstrated to be required for full copper resistance and regulated at the transcription level by Cu. Expression of copCD is regulated directly by the two-component response regulator CopR, which also regulates its own expression. Interruption of the regulated expression of copR affected bacterial growth, biofilm formation, and tissue dissemination and survival. A mutant CopR, which lacks the N-terminal signal receiver domain and is constitutively active, was found to have an attenuating effect on bacterial virulence when expressed in TSS. To our knowledge, this is the first report that suggests a link between CopR and bacterial pathogenicity in P. fluorescens.

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Bradyrhizobium spp. and Sinorhizobium fredii are Predominant in Root Nodules of Vigna angularis, a Native Legume Crop in the Subtropical Region of China: Li Li Han , En Tao Wang , Yang Li Lu , Yong Fa Zhang , Xin Hua Sui , Wen Feng Chen , Wen Xin Chen; J. Microbiol. 2009;47(3):287-296. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-009-0001-5

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Abstract

Adzuki bean (Vigna angularis) is an important legume crop native to China, but its rhizobia have not been well characterized. In the present study, a total of 60 rhizobial strains isolated from eight provinces of China were analyzed with amplified 16S rRNA gene RFLP, IGS-RFLP, and sequencing analyses of 16S rRNA, atpD, recA, and nodC genes. These strains were identified as genomic species within Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium, and Ochrobactrum. The most abundant groups were Bradyrhizobium species and Sinorhizobium fredii. Diverse nodC genes were found in these strains, which were mainly co-evolved with the housekeeping genes, but a possible lateral transfer of nodC from Sinorhizobium to Rhizobium was found. Analyses of the genomic and symbiotic gene backgrounds showed that adzuki bean shared the same rhizobial gene pool with soybean (legume native to China) and the exotic Vigna species. All of these data demonstrated that nodule formation is the interaction of rhizobia, host plants, and environment characters.

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Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance
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Expression and Regulation of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase Genes in Mycobacterium sp. Strain JC1 DSM 3803: Jae Ho Lee , Dong Oh Park , Sae Woong Park , Eun Ha Hwang , Jeong Il Oh , Young Min Kim; J. Microbiol. 2009;47(3):297-307. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0210-3

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Abstract

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is the key enzyme of the Calvin reductive pentose phosphate cycle. Two sets of structural genes (cbbLS-1 and -2) for form I RubisCO have been previously identified in the Mycobacterium sp. strain JC1, which is able to grow on carbon monoxide (CO) or methanol as sole sources of carbon and energy. Northern blot and reverse transcriptase PCR showed that the cbbLS-1 and -2 genes are expressed in cells grown on either carbon monoxide (CO) or methanol, but not in cells grown in nutrient broth. A promoter assay revealed that the cbbLS-2 promoter has a higher activity than the cbbLS-1 promoter in both CO- and methanol-grown cells, and that the activities of both promoters were higher in CO-grown cells than in methanol-grown cells. A gel mobility shift assay and footprinting assays showed that CbbR expressed in Escherichia coli from a cbbR gene, which is located downstream of cbbLS-1 and transcribed in the same orientation as that of the cbbLS genes, specifically bound to the promoter regions of the cbbLS-1 and -2 genes containing inverted repeat sequence. A DNase I footprinting assay revealed that CbbR protected positions -59 to -3 and -119 to -78 of the cbbLS-1 and -2 promoters, respectively. Overexpression of CbbR induced the transcription of RubisCO genes in Mycobacterium sp. strain JC1 grown in nutrient broth. Our results suggest that the CbbR product from a single cbbR gene may positively regulate two cbbLS operons in the Mycobacterium sp. strain JC1 as is the case for Rhodobacter sphaeroides and Cupriavidus necator.

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Abhishek Anil Dubey, Saloni Rajesh Wani, Vikas Jain, William W. Metcalf
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Antonie van Leeuwenhoek.2018; 111(8): 1403. CrossRef
Functional characterization of the cutI gene for the transcription of carbon monoxide dehydrogenase genes in Mycobacterium sp. strain JC1 DSM 3803
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CbbR, the Master Regulator for Microbial Carbon Dioxide Fixation
Andrew W. Dangel, F. Robert Tabita, W. Margolin
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Amino acid substitutions in the transcriptional regulator CbbR lead to constitutively active CbbR proteins that elevate expression of the cbb CO2 fixation operons in Ralstonia eutropha (Cupriavidus necator) and identify regions of CbbR necessary for gene
Andrew W. Dangel, F. Robert Tabita
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Gene Expression Analysis of Phanerochaete chrysosporium During the Transition Time from Primary Growth to Secondary Metabolism: Mingfeng Jiang , Xiao Li , Liang Zhang , Hong Feng , Yizheng Zhang; J. Microbiol. 2009;47(3):308-318. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0275-z

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Abstract

In order to identify the secondary metabolism-related genes of Phanerochaete chrysosporium growing under pure O2 and nitrogen-limited conditions, 2322 ESTs fragments originated from two suppression-subtractive libraries were analyzed using the cDNA microarray technique. Ten significantly upregulated and 22 significantly downregulated genes were identified in the 72 h cultured mycelia RNA samples (secondary metabolism). According to qPCR, 16 out of the 32 genes were expressed differently in secondary metabolism. Transcripts of secondary metabolism up-regulation genes exhibited homologies to aryl-alcohol dehydrogenase (SSh1554), ABC transporter gene (SSH624), chitinase (SSH963), heat shock protein (SSH1193), catalase (SSH317), cytochrome P450 (SSH331), glucosamine-6-phosphate isomerase (SSH611), and alkyl hydroperoxide reductase (SSH362) genes. Ninety-three genes could be classified by Eukaryotic Orthologous Groups (KOG). Among the genes assigned a function, gene expression patterns were different in both secondary metabolism and primary metabolism. In the group of “Cellular Processes and Signaling,” most of the genes were from the primary metabolism library. On the other hand, genes from the secondary metabolism library were found mainly in the “Information Storage” and “Processing and Poorly Characterized” groups. Based on the KOG functional assignments, six genes belong to the ubiquitin system, and all of them were from primary metabolism phase. The presence of the H2O2-relevant genes suggested that parts of the genes expressed in 72 h might be involved in the ligninolytic process during secondary metabolism of P. chrysosporium.

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The Gene bap, Involved in Biofilm Production, Is Present in Staphylococcus spp. Strains from Nosocomial Infections: Amina Potter , Hilana Ceotto , Marcia Giambiagi-deMarval , Katia Regina Netto dos Santos , Ingolf F. Nes , Maria do Carmo de Freire Bastos; J. Microbiol. 2009;47(3):319-326. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-009-0008-y

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Abstract

This study analyzed ten strains of coagulase-negative staphylococci (CNS) involved in nosocomial infections in three Brazilian hospitals. Their antibiotic susceptibility profile showed that most strains exhibited multiple antibiotic resistance and possessed the mecA gene. The ability of these strains to adhere to polystyrene microtiter plates was also tested and nine of them proved to be biofilm producers at least in one of the three conditions tested: growth in TSB, in TSB supplemented with NaCl, or in TSB supplemented with glucose. The presence of the bap gene, which codes for the biofilm-associated protein (Bap), was investigated in all ten strains by PCR. All strains were bap-positive and DNA sequencing experiments confirmed that the fragments amplified were indeed part of a bap gene. The presence of the icaA gene, one of the genes involved in polysaccharide intercellular adhesin (PIA) formation, was also detected by PCR in eight of the ten strains tested. The two icaA-negative strains were either weak biofilm producer or no biofilm producer, although they were bap-positive. To our knowledge, this is the first report demonstrating the presence of the bap gene in nosocomial isolates of CNS, being also the first report on the presence of this gene in Staphylococcus haemolyticus and S. cohnii.

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Journal Article

Mobilization Functions of the Bacteriocinogenic Plasmid pRJ6 of Staphylococcus aureus: Marcus Livio Varella Coelho , Hilana Ceotto , Danielle Jannuzzi Madureira , Ingolf F. Nes , Maria do Carmo de Freire Bastos; J. Microbiol. 2009;47(3):327-336. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-009-0044-7

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Abstract: Plasmid pRJ6 is the first known bacteriocinogenic mobilizable (Mob) plasmid of Staphylococcus aureus. Its Mob region is composed of four mob genes (mobCDAB) arranged as an operon, a genetic organization uncommon among S. aureus Mob plasmids. oriTpRJ6 was detected in a region of 431 bp, positioned immediately upstream of mobC. This region, when cloned into pCN37, was able to confer mobilization to the recombinant plasmid only in the presence of pRJ6. The entire Mob region, including oriTpRJ6, is much more similar to Mob regions from several coagulase-negative staphylococci plasmids, although some remarkable similarities with S. aureus Mob plasmids can also be noted. These similarities include the presence within oriTpRJ6 of the three mcb (MobC binding sites), firstly described in pC221 and pC223, an identical nick site also found in these same plasmids, and a nearly identical srapC223 site (sequence recognized by MobA). pRJ6 was successfully transferred to S. epidermidis by conjugation in the presence of the conjugative plasmid pGO1. Altogether these findings suggest that pRJ6 might have been originally a coagulase-negative staphylococci plasmid that had been transferred successfully to S. aureus.

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

Nup211, the Fission Yeast Homolog of Mlp1/Tpr, Is Involved in mRNA Export: Jin-Ah Bae , DongGeRaMi Moon , Jin Ho Yoon; J. Microbiol. 2009;47(3):337-343. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-009-0125-7

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Abstract

Synthetic lethal mutants have been previously isolated in fission yeast Schizosaccharomyces pombe, which genetically interact with spmex67, in order to identify the genes involved in mRNA export. The nup211 gene was isolated by complementation of the growth defect in one of the synthetic lethal mutants, SLMex2, under synthetic lethal condition. We showed that Nup211, fission yeast homolog of Mlp1/Mlp2/Tpr, is essential for vegetative growth and Nup211-GFP proteins expressed at endogenous level are localized mainly in nuclear periphery. The accumulation of poly(A)+ RNA in the nucleus is exhibited when expression of nup211 is repressed or over-expressed. These results suggest that the Nup211 protein plays a pivotal role of mRNA export in fission yeast.

Citations

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Exchange of the VP5 of Infectious Bursal Disease Virus in a Serotype I Strain with that of a Serotype II Strain Reduced the Viral Replication and Cytotoxicity: Liting Qin , Xiaole Qi , Honglei Gao , Yulong Gao , Zhigao Bu , Xiaomei Wang; J. Microbiol. 2009;47(3):344-350. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-009-0028-7

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Abstract: Infectious bursal disease virus (IBDV), belonging to Avibirnavirus genus in the Birnaviridae family, consists of two segments of double-strand RNA. There are two distinct serotypes of IBDV, the pathogenic serotypeI and the non-pathogenic serotype II. Comparison of the deduced amino acid sequences of a panel of VP5 genes retrieved from GenBank revealed a high identity among strains within the serotype I or serotypeII group but a low identity between strains across two serotypes. In this study, we rescued two mosaic viruses, rGtGxVP5 and rGt2382VP5 by exchanging the VP5 gene of a cell culture-adapted serotype I Gt strain with its counterpart of the very virulent IBDV Gx strain, or a non-pathogenic 23/82 strain of the serotype II. In comparison to the parental strain rGt virus, the rGtGxVP5 showed the similar viral replication, cytotoxicity and the ability of inducing apoptosis; however, the other mosaic virus rGt2382VP5 had a lower titer and a reduced cytotoxicity. Although exchange of VP5 within serotype I group did not alter the viral replication and cytotoxicity of Gt strain, exchange of VP5 in the serotype I with that of a serotypeII reduced the viral replication and cytotoxicity on chicken embryo fibroblast (CEF) cells. Therefore, the VP5 of serotype II may be one of the factors responsible for the distinct pathogenic features of two serotypes.

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