scholarly journals An Inducible Operon Is Involved in Inulin Utilization in Lactobacillus plantarum Strains, as Revealed by Comparative Proteogenomics and Metabolic Profiling

2016 ◽  
Vol 83 (2) ◽  
Author(s):  
Nirunya Buntin ◽  
Tipparat Hongpattarakere ◽  
Jarmo Ritari ◽  
François P. Douillard ◽  
Lars Paulin ◽  
...  
Keyword(s):  
Cell Wall ◽  
Lactobacillus Plantarum ◽  
Functional Characteristic ◽  
Fermented Foods ◽  
Sucrose Transport ◽  
Protein Coding ◽  
Content Type ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Infant Feces

ABSTRACT The draft genomes of Lactobacillus plantarum strains isolated from Asian fermented foods, infant feces, and shrimp intestines were sequenced and compared to those of well-studied strains. Among 28 strains of L. plantarum, variations in the genomic features involved in ecological adaptation were elucidated. The genome sizes ranged from approximately 3.1 to 3.5 Mb, of which about 2,932 to 3,345 protein-coding sequences (CDS) were predicted. The food-derived isolates contained a higher number of carbohydrate metabolism-associated genes than those from infant feces. This observation correlated to their phenotypic carbohydrate metabolic profile, indicating their ability to metabolize the largest range of sugars. Surprisingly, two strains (P14 and P76) isolated from fermented fish utilized inulin. β-Fructosidase, the inulin-degrading enzyme, was detected in the supernatants and cell wall extracts of both strains. No activity was observed in the cytoplasmic fraction, indicating that this key enzyme was either membrane-bound or extracellularly secreted. From genomic mining analysis, a predicted inulin operon of fosRABCDXE, which encodes β-fructosidase and many fructose transporting proteins, was found within the genomes of strains P14 and P76. Moreover, pts1BCA genes, encoding sucrose-specific IIBCA components involved in sucrose transport, were also identified. The proteomic analysis revealed the mechanism and functional characteristic of the fosRABCDXE operon involved in the inulin utilization of L. plantarum. The expression levels of the fos operon and pst genes were upregulated at mid-log phase. FosE and the LPXTG-motif cell wall anchored β-fructosidase were induced to a high abundance when inulin was present as a carbon source. IMPORTANCE Inulin is a long-chain carbohydrate that may act as a prebiotic, which provides many health benefits to the host by selectively stimulating the growth and activity of beneficial bacteria in the colon. While certain lactobacilli can catabolize inulin, this has not yet been described for Lactobacillus plantarum, and an associated putative inulin operon has not been reported in this species. By using comparative and functional genomics, we showed that two L. plantarum strains utilized inulin and identified functional inulin operons in their genomes. The proteogenomic data revealed that inulin degradation and uptake routes, which related to the fosRABCDXE operon and pstBCA genes, were widely expressed among L. plantarum strains. The present work provides a novel understanding of gene regulation and mechanisms of inulin utilization in probiotic L. plantarum generating opportunities for synbiotic product development.

scholarly journals Complete Genome Sequence of Bacillus vallismortis NBIF-001, a Novel Strain from Shangri-La, China, That Has High Activity against Fusarium oxysporum

2017 ◽  
Vol 5 (48) ◽  
Author(s):  
Xiaoyan Liu ◽  
Yong Min ◽  
Daye Huang ◽  
Ronghua Zhou ◽  
Wei Fang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Positive Bacterium ◽  
Protein Coding ◽  
Content Type ◽  
Number Of Genes ◽  
Genes Encoding ◽  
Bacillus Vallismortis ◽  
Rna Genes

ABSTRACT Bacillus vallismortis NBIF-001, a Gram-positive bacterium, was isolated from soil in Shangri-La, China. Here, we provide the complete genome sequence of this bacterium, which has a 3,929,787-bp-long genome, including 4,030 protein-coding genes and 195 RNA genes. This strain possesses a number of genes encoding virulence factors of pathogens.

scholarly journals Staphylococcus epidermidis MSCRAMM SesJ Is Encoded in Composite Islands

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Srishtee Arora ◽  
Xiqi Li ◽  
Andrew Hillhouse ◽  
Kranti Konganti ◽  
Sara V. Little ◽  
...  
Keyword(s):  
Cell Wall ◽  
Antibiotic Resistance ◽  
Virulence Factors ◽  
Staphylococcus Epidermidis ◽  
Core Genome ◽  
Clinical Isolates ◽  
Modification System ◽  
Content Type ◽  
Genes Encoding ◽  
Staphylococcal Cassette Chromosome

ABSTRACT Staphylococcus epidermidis is a leading cause of nosocomial infections in patients with a compromised immune system and/or an implanted medical device. Seventy to 90% of S. epidermidis clinical isolates are methicillin resistant and carry the mecA gene, present in a mobile genetic element (MGE) called the staphylococcal cassette chromosome mec (SCCmec) element. Along with the presence of antibiotic and heavy metal resistance genes, MGEs can also contain genes encoding secreted or cell wall-anchored virulence factors. In our earlier studies of S. epidermidis clinical isolates, we discovered S. epidermidis surface protein J (SesJ), a prototype of a recently discovered subfamily of the microbial surface component recognizing adhesive matrix molecule (MSCRAMM) group. MSCRAMMs are major virulence factors of pathogenic Gram-positive bacteria. Here, we report that the sesJ gene is always accompanied by two glycosyltransferase genes, gtfA and gtfB, and is present in two MGEs, called the arginine catabolic mobile element (ACME) and the staphylococcal cassette chromosome (SCC) element. The presence of the sesJ gene was associated with the left-hand direct repeat DR_B or DR_E. When inserted via DR_E, the sesJ gene was encoded in the SCC element. When inserted via DR_B, the sesJ gene was accompanied by the genes for the type 1 restriction modification system and was encoded in the ACME. Additionally, the SCC element and ACME carry different isoforms of the SesJ protein. To date, the genes encoding MSCRAMMs have been seen to be located in the bacterial core genome. Here, we report the presence of an MSCRAMM in an MGE in S. epidermidis clinical isolates. IMPORTANCE S. epidermidis is an opportunistic bacterium that has established itself as a successful nosocomial pathogen. The modern era of novel therapeutics and medical devices has extended the longevity of human life, but at the same time, we also witness the evolution of pathogens to adapt to newly available niches in the host. Increasing antibiotic resistance among pathogens provides an example of such pathogen adaptation. With limited opportunities to modify the core genome, most of the adaptation occurs by acquiring new genes, such as virulence factors and antibiotic resistance determinants present in MGEs. In this study, we describe that the sesJ gene, encoding a recently discovered cell wall-anchored protein in S. epidermidis, is present in both ACME and the SCC element. The presence of virulence factors in MGEs can influence the virulence potential of a specific strain. Therefore, it is critical to study the virulence factors found in MGEs in emerging pathogenic bacteria or strains to understand the mechanisms used by these bacteria to cause infections.

scholarly journals Direct Target Network of the Neurospora crassa Plant Cell Wall Deconstruction Regulators CLR-1, CLR-2, and XLR-1

mBio ◽  
2015 ◽  
Vol 6 (5) ◽  
Author(s):  
James P. Craig ◽  
Samuel T. Coradetti ◽  
Trevor L. Starr ◽  
N. Louise Glass
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Transcription Factors ◽  
Neurospora Crassa ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Nutrient Sensing ◽  
Wall Material ◽  
Content Type ◽  
Genes Encoding

ABSTRACTFungal deconstruction of the plant cell requires a complex orchestration of a wide array of intracellular and extracellular enzymes. InNeurospora crassa, CLR-1, CLR-2, and XLR-1 have been identified as key transcription factors regulating plant cell wall degradation in response to soluble sugars. The XLR-1 regulon was defined using a constitutively active mutant allele, resulting in hemicellulase gene expression and secretion under noninducing conditions. To define genes directly regulated by CLR-1, CLR-2, and XLR-1, we performed chromatin immunoprecipitation and next-generation sequencing (ChIPseq) on epitope-tagged constructs of these three transcription factors. WhenN. crassais exposed to plant cell wall material, CLR-1, CLR-2, and XLR-1 individually bind to the promoters of the most strongly induced genes in their respective regulons. These include promoters of genes encoding cellulases for CLR-1 and CLR-2 (CLR-1/CLR-2) and promoters of genes encoding hemicellulases for XLR-1. CLR-1 bound to its regulon under noninducing conditions; however, this binding alone did not translate into gene expression and enzyme secretion. Motif analysis of the bound genes revealed conserved DNA binding motifs, with the CLR-2 motif matching that of its closest paralog inSaccharomyces cerevisiae, Gal4p. Coimmunoprecipitation studies showed that CLR-1 and CLR-2 act in a homocomplex but not as a CLR-1/CLR-2 heterocomplex.IMPORTANCEUnderstanding fungal regulation of complex plant cell wall deconstruction pathways in response to multiple environmental signals via interconnected transcriptional circuits provides insight into fungus/plant interactions and eukaryotic nutrient sensing. Coordinated optimization of these regulatory networks is likely required for optimal microbial enzyme production.

scholarly journals Complete Genome Sequence of Lactobacillus plantarum Strain JDARSH, Isolated from Sheep Milk

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Abhinandan Patil ◽  
Anamika Dubey ◽  
Muneer Ahmad Malla ◽  
John Disouza ◽  
Shivaji Pawar ◽  
...  
Keyword(s):  
Lactobacillus Plantarum ◽  
Genome Sequence ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Sheep Milk ◽  
Wide Range ◽  
Range Of Functions

Lactobacillus plantarum strain JDARSH, a potential probiotic with a wide range of functions, was isolated from sheep milk. Here, we report the whole-genome sequence of this bacterium. The draft genome yielded a 3.20-Mb genome and 2,980 protein-coding sequences.

scholarly journals Human IgM Inhibits the Formation of Titan-Like Cells in Cryptococcus neoformans

2020 ◽  
Vol 88 (4) ◽  
Author(s):  
Nuria Trevijano-Contador ◽  
Kaila M. Pianalto ◽  
Connie B. Nichols ◽  
Oscar Zaragoza ◽  
J. Andrew Alspaugh ◽  
...  
Keyword(s):  
Cell Wall ◽  
Stress Response ◽  
B Cell ◽  
Cryptococcus Neoformans ◽  
Cell Formation ◽  
Transcriptional Analysis ◽  
Content Type ◽  
Human Immunoglobulins ◽  
Genes Encoding

ABSTRACT Human studies have shown associations between cryptococcal meningitis and reduced IgM memory B cell levels, and studies in IgM- and/or B cell-deficient mice have demonstrated increased Cryptococcus neoformans dissemination from lungs to brain. Since immunoglobulins are part of the immune milieu that C. neoformans confronts in a human host, and its ability to form titan cells is an important virulence mechanism, we determined the effect of human immunoglobulins on C. neoformans titan cell formation in vitro. (i) Fluorescence microscopy showed normal human IgG and IgM bind C. neoformans. (ii) C. neoformans grown in titan cell-inducing medium with IgM, not IgG, inhibited titan-like cell formation. (iii) Absorption of IgM with laminarin or curdlan (branched and linear 1-3-beta-d-glucans, respectively) decreased this effect. (iv) Transmission electron microscopy revealed that cells grown with IgM had small capsules and unique features not seen with cells grown with IgG. (v) Comparative transcriptional analysis of cell wall, capsule, and stress response genes showed that C. neoformans grown with IgM, not IgG or phosphate-buffered saline (PBS), had decreased expression of chitin synthetase, CHS1, CHS2, and CHS8, and genes encoding cell wall carbohydrate synthetases α-1-3-glucan (AGS1) and β-1,3-glucan (FKS1). IgM also decreased expression of RIM101 and HOG1, genes encoding central regulators of C. neoformans stress response pathways and cell morphogenesis. Our data show human IgM affects C. neoformans morphology in vitro and suggest that the hypothesis that human immunoglobulins may affect C. neoformans virulence in vivo warrants further investigation.

scholarly journals Gene Models, Expression Repertoire, and Immune Response of Plasmodium vivax Reticulocyte Binding Proteins

2015 ◽  
Vol 84 (3) ◽  
pp. 677-685 ◽  
Author(s):  
Jenni Hietanen ◽  
Anongruk Chim-ong ◽  
Thanprakorn Chiramanewong ◽  
Jakub Gruszczyk ◽  
Wanlapa Roobsoong ◽  
...  
Keyword(s):  
Plasmodium Vivax ◽  
Significant Negative Correlation ◽  
Protein Coding ◽  
Content Type ◽  
Immune Pressure ◽  
The Family ◽  
Genes Encoding ◽  
Gene Models

Members of thePlasmodium vivaxreticulocyte binding protein (PvRBP) family are believed to mediate specific invasion of reticulocytes byP. vivax. In this study, we performed molecular characterization of genes encoding members of this protein family. Through cDNA sequencing, we constructed full-length gene models and verified genes that are protein coding and those that are pseudogenes. We also used quantitative PCR to measure theirin vivotranscript abundances in clinicalP. vivaxisolates. Like genes encoding related invasion ligands ofP. falciparum,Pvrbpexpression levels vary broadly across different parasite isolates. Through antibody measurements, we found that host immune pressure may be the driving force behind the distinctly high diversity of one of the family members, PvRBP2c. Mild yet significant negative correlation was found between parasitemia and the PvRBP2b antibody level, suggesting that antibodies to the protein may interfere with invasion.

scholarly journals Cephem Potentiation by Inactivation of Nonessential Genes Involved in Cell Wall Biogenesis of β-Lactamase-Producing Escherichia coli

2016 ◽  
Vol 61 (3) ◽  
Author(s):  
Kristin R. Baker ◽  
Helga Høeg Sigurðardóttir ◽  
Bimal Jana ◽  
Luca Guardabassi
Keyword(s):  
Escherichia Coli ◽  
Cell Wall ◽  
Lag Phase ◽  
Growth Curve Analysis ◽  
Wild Type ◽  
Content Type ◽  
Cell Wall Biogenesis ◽  
Genes Encoding ◽  
In The Wild ◽  
Nonessential Genes

ABSTRACT Reversal of antimicrobial resistance is an appealing and largely unexplored strategy in drug discovery. The objective of this study was to identify potential targets for “helper” drugs reversing cephem resistance in Escherichia coli strains producing β-lactamases. A CMY-2-encoding plasmid was transferred by conjugation to seven isogenic deletion mutants exhibiting cephem hypersusceptibility. The effect of each mutation was evaluated by comparing the MICs in the wild type and the mutant harboring the same plasmid. Mutation of two genes encoding proteins involved in cell wall biosynthesis, dapF and mrcB, restored susceptibility to cefoxitin (FOX) and reduced the MICs of cefotaxime and ceftazidime, respectively, from the resistant to the intermediate category according to clinical breakpoints. The same mutants harboring a CTX-M-1-encoding plasmid fell into the intermediate or susceptible category for all three drugs. Individual deletion of dapF and mrcB in a clinical isolate of CTX-M-15-producing E. coli sequence type 131 (ST131) resulted in partial reversal of ceftazidime and cefepime resistance but did not reduce MICs below susceptibility breakpoints. Growth curve analysis indicated no fitness cost in a ΔmrcB mutant, whereas a ΔdapF mutant had a 3-fold longer lag phase than the wild type, suggesting that drugs targeting DapF may display antimicrobial activity, in addition to synergizing with selected cephems. DapF appeared to be a potential FOX helper drug target candidate, since dapF inactivation resulted in synergistic potentiation of FOX in the genetic backgrounds tested. The study showed that individual inactivation of two nonessential genes involved in cell wall biogenesis potentiates cephem activity according to drug- and strain-specific patterns.

scholarly journals Draft Genome Sequence of Lactobacillus plantarum EBKLp545, Isolated from Piglet Feces

2019 ◽  
Vol 8 (16) ◽  
Author(s):  
Sukjung Choi ◽  
Eun Bae Kim
Keyword(s):  
South Korea ◽  
Lactobacillus Plantarum ◽  
Genome Sequence ◽  
Noncoding Rna ◽  
Draft Genome ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Rna Genes

Lactobacillus plantarum strain EBKLp545 was isolated from piglet feces in South Korea and sequenced using an Illumina HiSeq system. This draft genome of strain EBKLp545 consists of 3,306,513 bp with 3,049 protein-coding genes in 138 contigs (≥500 bp), 54 noncoding RNA genes, and a 44.3% G+C content.

scholarly journals Effects of the Peptide Pheromone Plantaricin A and Cocultivation with Lactobacillus sanfranciscensis DPPMA174 on the Exoproteome and the Adhesion Capacity of Lactobacillus plantarum DC400

2013 ◽  
Vol 79 (8) ◽  
pp. 2657-2669 ◽  
Author(s):  
Maria Calasso ◽  
Raffaella Di Cagno ◽  
Maria De Angelis ◽  
Daniela Campanella ◽  
Fabio Minervini ◽  
...  
Keyword(s):  
Cell Wall ◽  
Lactobacillus Plantarum ◽  
Defined Medium ◽  
Extracellular Proteins ◽  
Phenotypic Traits ◽  
Two Dimensional Gel Electrophoresis ◽  
Content Type ◽  
Lactobacillus Sanfranciscensis ◽  
Associated Proteins ◽  
Intestinal Pathogens

ABSTRACTThis study aimed at investigating the extracellular and cell wall-associated proteins (exoproteome) ofLactobacillus plantarumDC400 when cultivated on modified chemically defined medium (CDM) supplemented with the chemically synthesized pheromone plantaricin A (PlnA) or cocultured withL. plantarumDPPMA20 orLactobacillus sanfranciscensisDPPMA174. Compared to monoculture, two-dimensional gel electrophoresis (2-DE) analysis showed that the exoproteome ofL. plantarumDC400 was affected by PlnA and cocultivation with strains DPPMA20 and, especially, DPPMA174. The highest similarity of the 2-DE maps was found between DC400 cells cultivated in monoculture and in coculture with strain DPPMA20. Almost all extracellular proteins (22 spots) and cell wall-associated proteins (40 spots) which showed decreased or increased levels of synthesis during growth in CDM supplemented with PlnA and/or in coculture with strain DPPMA20 or DPPMA174 were identified. On the basis of the sequences in the Kyoto Encyclopedia of Genes and Genomes database, changes to the exoproteome concerned proteins involved in quorum sensing (QS), the transport system, stress response, carbohydrate metabolism and glycolysis, oxidation/reduction processes, the proteolytic system, amino acid metabolism, cell wall and catabolic processes, and cell shape, growth, and division. Cultivation with PlnA and cocultivation with strains DPPMA20 and, especially, DPMMA174 markedly increased the capacity ofL. plantarumDC400 to form biofilms, to adhere to human Caco-2 cells, and to prevent the adhesion of potential intestinal pathogens. These phenotypic traits were in part related to oversynthesized moonlighting proteins (e.g., DnaK and GroEL, pyruvate kinase, enolase, and glyceraldehyde-3-phosphate dehydrogenase) in response to QS mechanisms and interaction withL. plantarumDPPMA20 and, especially,L. sanfranciscensisDPPMA174.

scholarly journals Role of Transcription Factor CaNdt80p in Cell Separation, Hyphal Growth, and Virulence in Candida albicans

2010 ◽  
Vol 9 (4) ◽  
pp. 634-644 ◽  
Author(s):  
Adnane Sellam ◽  
Christopher Askew ◽  
Elias Epp ◽  
Faiza Tebbji ◽  
Alaka Mullick ◽  
...  
Keyword(s):  
Cell Wall ◽  
Transcription Factor ◽  
Candida Albicans ◽  
Cell Separation ◽  
Hyphal Growth ◽  
Functional Domain ◽  
Transcription Factor Family ◽  
Content Type ◽  
Genes Encoding

ABSTRACT The NDT80/PhoG transcription factor family includes ScNdt80p, a key modulator of the progression of meiotic division in Saccharomyces cerevisiae. In Candida albicans, a member of this family, CaNdt80p, modulates azole sensitivity by controlling the expression of ergosterol biosynthesis genes. We previously demonstrated that CaNdt80p promoter targets, in addition to ERG genes, were significantly enriched in genes related to hyphal growth. Here, we report that CaNdt80p is indeed required for hyphal growth in response to different filament-inducing cues and for the proper expression of genes characterizing the filamentous transcriptional program. These include noteworthy genes encoding cell wall components, such as HWP1, ECE1, RBT4, and ALS3. We also show that CaNdt80p is essential for the completion of cell separation through the direct transcriptional regulation of genes encoding the chitinase Cht3p and the cell wall glucosidase Sun41p. Consistent with their hyphal defect, ndt80 mutants are avirulent in a mouse model of systemic candidiasis. Interestingly, based on functional-domain organization, CaNdt80p seems to be a unique regulator characterizing fungi from the CTG clade within the subphylum Saccharomycotina. Therefore, this study revealed a new role of the novel member of the fungal NDT80 transcription factor family as a regulator of cell separation, hyphal growth, and virulence.

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