Glutamine synthetase gene expression at elevated hydrostatic pressure in a deep-sea piezophilic Shewanella violacea

Physiological and genomic features of Paraoceanicella profunda gen. nov., sp. nov., a novel piezophile isolated from deep seawater of the Mariana Trench

A novel piezophilic alphaproteobacterium, strain D4M1^T, was isolated from deep seawater of the Mariana Trench. 16S rRNA gene analysis showed that strain D4M1^T was most closely related to Oceanicella actignis PRQ‐67^T (94.2%), Oceanibium sediminis O448^T (94.2%), and Thioclava electrotropha ElOx9^T (94.1%). Phylogenetic analyses based on both 16S rRNA gene and genome sequences showed that strain D4M1^T formed an independent monophyletic branch paralleled with the genus Oceanicella in the family Rhodobacteraceae. Cells were Gram‐stain‐negative, aerobic short rods, and grew optimally at 37°C, pH 6.5, and 3.0% (w/v) NaCl. Strain D4M1^T was piezophilic with the optimum pressure of 10 MPa. The principal fatty acids were C_18:1ω7c/C_18:1ω6c and C_16:0, major respiratory quinone was ubiquinone‐10, and predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminophospholipid. The complete genome contained 5,468,583‐bp with a G + C content of 70.2 mol% and contained 4,855 protein‐coding genes and 78 RNA genes. Genomic analysis revealed abundant clues on bacterial high‐pressure adaptation and piezophilic lifestyle. The combined evidence shows that strain D4M1^T represents a novel species of a novel genus in the family Rhodobacteraceae, for which the name Paraoceanicella profunda gen. nov., sp. nov. is proposed (type strain D4M1^T = MCCC 1K03820^T = KCTC 72285^T).

VdThit, a Thiamine Transport Protein, Is Required for Pathogenicity of the Vascular Pathogen Verticillium dahliae

Verticillium dahliae causes a serious wilt disease of important crops and is difficult to control. Few plasma-membrane transport proteins for nutrient acquisition have been identified for this fungus, and their involvement in the disease process is unknown. Here, a plasma-membrane protein, the V. dahliae thiamine transporter protein VdThit, was characterized functionally by deletion of the VdThit gene in V. dahliae. Disruption strains were viable, but growth and conidial germination and production were reduced and virulence was impaired. Interestingly, by supplementing exogenous thiamine, growth, conidiation, and virulence of the VdΔThit mutants were partially restored. Stress-tolerance assays showed that the VdΔThit mutant strains were markedly more susceptible to oxidative stress and UV damage. High-pressure liquid chromatography-mass spectrometry (HPLC-MS) and gas chromatography-mass spectrometry (GC-MS) analyses showed low levels of pyruvate metabolism intermediates acetoin and acetyl coenzyme A (acetyl-CoA) in the VdΔThit mutant strains, suggesting that pyruvate metabolism was suppressed. Expression analysis of VdThit confirmed the importance of VdThit in vegetative growth, reproduction, and invasive hyphal growth. Furthermore, a green fluorescent protein (GFP)-labeled VdΔThit mutant (VdΔThit-7-GFP) was suppressed in initial infection and root colonization, as viewed with light microscopy. Together, these results showed that VdThit plays an indispensable role in the pathogenicity of V. dahliae.

Genomic analysis of Luteimonas abyssi XH031(T): insights into its adaption to the subseafloor environment of South Pacific Gyre and ecological role in biogeochemical cycle

Background

Luteimonas abyssi XH031^T, which was previously isolated from subseafloor environment of the South Pacific Gyre (SPG), was an aerobic, gram-negative bacterium, and was identified to be a novel species of the genus Luteimonas in the family of Xanthomonadaceae. The nutrients utilization and metabolic mechanisms of XH031^T indicate its plasticity. In view of the above characteristics, its genome was sequenced, and an in-depth analysis of the XH031^T genome was performed to elucidate its adaption to extreme ecological environment.

Results

Various macromolecules including polysaccharide, protein, lipid and DNA could be degraded at low temperature by XH031^T under laboratory conditions, and its degradation abilities to starch, gelatin and casein were considerably strong. Genome sequence analysis indicated that XH031^T possesses extensive enzyme-encoding genes compared with four other Luteimonas strains. In addition, intricate systems (such as two-component regulatory systems, secretion systems, etc.), which are often used by bacteria to modulate the interactions of bacteria with their environments, were predicted in the genome of XH031^T. Genes encoding a choline-glycine betaine transporter and 99 extracellular peptidases featured with halophilicity were predicted in the genome, which might help the bacterium to adapt to the salty marine environment. Moreover, there were many gene clusters in the genome encoding ATP-binding cassette superfamily transporters, major facilitator superfamily transporters and cytochrome P450s that might function in the process of various substrate transportation and metabolisms. Furthermore, drug resistance genes harbored in the genome might signify that XH031^T has evolved hereditary adaptation to toxic environment. Finally, the annotation of metabolic pathways of the elements (such as carbon, nitrogen, sulfur, phosphor and iron) in the genome elucidated the degradation of organic matter in the deep sediment of the SPG.

Conclusions

The genome analysis showed that XH031^T had genetic advantages to adapt to subseafloor environment. The material metabolism manifests that the strain may play an important ecological role in the biogeochemical cycle of the SPG, and various cold-adapted extracelluar enzymes produced by the strain may have significant value in application.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2326-2) contains supplementary material, which is available to authorized users.

Isoleucine 61 is important for the hemolytic activity of pyolysin of Trueperella pyogenes

Pyolysin (PLO) is a hemolysin secreted by Trueperella pyogenes (T. pyogenes) and is important for the pathogenicity of T. pyogenes. Oligomerization of PLO monomers is a critical step in the process of hemolysis. However, the mechanisms of intermolecular interaction of PLO monomers are still not clearly illuminated. In this study, two monoclonal antibodies (mAbs) against PLO, named AP-1A3 and AP-4F12, respectively, were generated firstly, of which AP-1A3 showed no or undetectable hemolysis inhibition activity against recombinant PLO (rPLO), whereas AP-4F12 could markedly inhibit the hemolytic activity of rPLO. Epitope mapping revealed that AP-1A3 recognized amino acid residues ranging from 64 to 79 of mature PLO (91-106 including the signal peptide), whereas AP-4F12 recognized amino acid residues ranging from 58 to 75 (85-102 including the signal peptide). Comparison of the amino acid sequence of two epitopes revealed that six amino acid residues ranging from 58 to 63 of PLO were associated with the hemolytic activity of PLO. Alanine scan showed that substitution of each amino acid ranging from 58 to 62 with alanine had apparent impact on the hemolytic activity of rPLO, especially for the substitution of isoleucine 61 which caused almost complete loss of hemolytic activity of rPLO. Our findings identified a region in PLO and an amino acid in that region might play important role in the process of oligomerization of PLO monomers.

Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure

RNA-seq was used to study the response of Desulfovibrio hydrothermalis, isolated from a deep-sea hydrothermal chimney on the East-Pacific Rise at a depth of 2,600 m, to various hydrostatic pressure growth conditions. The transcriptomic datasets obtained after growth at 26, 10 and 0.1 MPa identified only 65 differentially expressed genes that were distributed among four main categories: aromatic amino acid and glutamate metabolisms, energy metabolism, signal transduction, and unknown function. The gene expression patterns suggest that D. hydrothermalis uses at least three different adaptation mechanisms, according to a hydrostatic pressure threshold (HP_t) that was estimated to be above 10 MPa. Both glutamate and energy metabolism were found to play crucial roles in these mechanisms. Quantitation of the glutamate levels in cells revealed its accumulation at high hydrostatic pressure, suggesting its role as a piezolyte. ATP measurements showed that the energy metabolism of this bacterium is optimized for deep-sea life conditions. This study provides new insights into the molecular mechanisms linked to hydrostatic pressure adaptation in sulfate-reducing bacteria.

Deep-sea natural products

This review covers the 390 novel marine natural products described to date from deep-water (>50 m) marine fauna, with details on the source organism, its depth and country of origin, along with any reported biological activity of the metabolites. Relevant synthetic studies on the deep-sea natural products have also been included.

Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation

The chemolithotrophic ammonia-oxidizing bacterium Nitrosomonas europaea is known to be highly resistant to starvation conditions. The transcriptional response of N. europaea to ammonia addition following short- and long-term starvation was examined by primer extension and S1 nuclease protection analyses of genes encoding enzymes for ammonia oxidation (amoCAB operons) and CO(2) fixation (cbbLS), a third, lone copy of amoC (amoC(3)), and two representative housekeeping genes (glyA and rpsJ). Primer extension analysis of RNA isolated from growing, starved, and recovering cells revealed two differentially regulated promoters upstream of the two amoCAB operons. The distal sigma(70) type amoCAB promoter was constitutively active in the presence of ammonia, but the proximal promoter was only active when cells were recovering from ammonia starvation. The lone, divergent copy of amoC (amoC(3)) was expressed only during recovery. Both the proximal amoC(1,2) promoter and the amoC(3) promoter are similar to gram-negative sigma(E) promoters, thus implicating sigma(E) in the regulation of the recovery response. Although modeling of subunit interactions suggested that a nonconservative proline substitution in AmoC(3) may modify the activity of the holoenzyme, characterization of a DeltaamoC(3) strain showed no significant difference in starvation recovery under conditions evaluated. In contrast to the amo transcripts, a delayed appearance of transcripts for a gene required for CO(2) fixation (cbbL) suggested that its transcription is retarded until sufficient energy is available. Overall, these data revealed a programmed exit from starvation likely involving regulation by sigma(E) and the coordinated regulation of catabolic and anabolic genes.

Heat shock protein-mediated resistance to high hydrostatic pressure in Escherichia coli

A random library of Escherichia coli MG1655 genomic fragments fused to a promoterless green fluorescent protein (GFP) gene was constructed and screened by differential fluorescence induction for promoters that are induced after exposure to a sublethal high hydrostatic pressure stress. This screening yielded three promoters of genes belonging to the heat shock regulon (dnaK, lon, clpPX), suggesting a role for heat shock proteins in protection against, and/or repair of, damage caused by high pressure. Several further observations provide additional support for this hypothesis: (i). the expression of rpoH, encoding the heat shock-specific sigma factor sigma(32), was also induced by high pressure; (ii). heat shock rendered E. coli significantly more resistant to subsequent high-pressure inactivation, and this heat shock-induced pressure resistance followed the same time course as the induction of heat shock genes; (iii). basal expression levels of GFP from heat shock promoters, and expression of several heat shock proteins as determined by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of proteins extracted from pulse-labeled cells, was increased in three previously isolated pressure-resistant mutants of E. coli compared to wild-type levels.

Differential pressure resistance in the activity of RNA polymerase isolated from Shewanella violacea and Escherichia coli

RNA polymerase was purified from the piezophile Shewanella violacea DSS12, and the transcriptional activity after pressure treatment was compared with that of the mesophile Escherichia coli. Application of pressure at 100 MPa for 30 min reduced the E. coli RNA polymerase activity to 60% of the activity at atmospheric pressure, whereas the S. violacea RNA polymerase maintained full activity, indicating that the S. violacea RNA polymerase is more stable than its E. coli counterpart. This result was supported by the analysis of the strength of subunit interactions of the enzyme from both species, using a high-pressure electrophoresis apparatus, which showed that a pressure of 140 MPa caused dissociation of E. coli RNA polymerase but not that of S. violacea RNA polymerase. On the other hand, the core enzyme of S. violacea RNA polymerase, which lacked the sigma70 factor, was dissociated at 140 MPa. These results suggest that the sigma70 factor is required for stabilization of S. violacea RNA polymerase under high-pressure conditions. In this paper, we provide in vitro evidence for piezoadaptation at the transcriptional level, using purified RNA polymerase from cells of S. violacea and E. coli.

Type II protein secretion is a subset of the PilD-dependent processes that facilitate intracellular infection by Legionella pneumophila

Previously, we had demonstrated that a Legionella pneumophila prepilin peptidase (pilD) mutant does not produce type IV pili and shows reduced secretion of enzymatic activities. Moreover, it displays a distinct colony morphology and a dramatic reduction in intracellular growth within amoebae and macrophages, two phenotypes that are not exhibited by a pilin (pilE(L)) mutant. To determine whether these pilD-dependent defects were linked to type II secretion, we have constructed two new mutants of L. pneumophila strain 130b. Mutations were introduced into either lspDE, which encodes the type II outer membrane secretin and ATPase, or lspFGHIJK, which encodes the pseudopilins. Unlike the wild-type and pilE(L) strains, both lspDE and lspG mutants showed reduced secretion of six pilD-dependent enzymatic activities; i.e., protease, acid phosphatase, p-nitrophenol phosphorylcholine hydrolase, lipase, phospholipase A, and lysophospholipase A. However, they exhibited a colony morphology different from that of the pilD mutant, suggesting that their surfaces are distinct. The pilD, lspDE, and lspG mutants were similarly and greatly impaired for growth within Hartmannella vermiformis, indicating that the intracellular defect of the peptidase mutant in amoebae is explained by the loss of type II secretion. When assessed for infection of U937 macrophages, both lsp mutants exhibited a 10-fold reduction in intracellular multiplication and a diminished cytopathic effect. Interestingly, the pilD mutant was clearly 100-fold more defective than the type II secretion mutants in U937 cells. These results suggest the existence of a novel pilD-dependent mechanism for promoting L. pneumophila intracellular infection of human cells.