Lactobacillus-dominated cervicovaginal microbiota associated with reduced HIV/STI prevalence and genital HIV viral load in African women

Cervicovaginal microbiota not dominated by lactobacilli may facilitate transmission of HIV and other sexually transmitted infections (STIs), as well as miscarriages, preterm births and sepsis in pregnant women. However, little is known about the exact nature of the microbiological changes that cause these adverse outcomes. In this study, cervical samples of 174 Rwandan female sex workers were analyzed cross-sectionally using a phylogenetic microarray. Furthermore, HIV-1 RNA concentrations were measured in cervicovaginal lavages of 58 HIV-positive women among them. We identified six microbiome clusters, representing a gradient from low semi-quantitative abundance and diversity dominated by Lactobacillus crispatus (cluster R-I, with R denoting 'Rwanda') and L. iners (R-II) to intermediate (R-V) and high abundance and diversity (R-III, R-IV and R-VI) dominated by a mixture of anaerobes, including Gardnerella, Atopobium and Prevotella species. Women in cluster R-I were less likely to have HIV (P=0.03), herpes simplex virus type 2 (HSV-2; P<0.01), and high-risk human papillomavirus (HPV; P<0.01) and had no bacterial STIs (P=0.15). Statistically significant trends in prevalence of viral STIs were found from low prevalence in cluster R-I, to higher prevalence in clusters R-II and R-V, and highest prevalence in clusters R-III/R-IV/R-VI. Furthermore, only 10% of HIV-positive women in clusters R-I/R-II, compared with 40% in cluster R-V, and 42% in clusters R-III/R-IV/R-VI had detectable cervicovaginal HIV-1 RNA (Ptrend=0.03). We conclude that L. crispatus-dominated, and to a lesser extent L. iners-dominated, cervicovaginal microbiota are associated with a lower prevalence of HIV/STIs and a lower likelihood of genital HIV-1 RNA shedding.

Transcriptional activity around bacterial cell death reveals molecular biomarkers for cell viability

Background

In bacteriology, the ability to grow in selective media and to form colonies on nutrient agar plates is routinely used as a retrospective criterion for the detection of living bacteria. However, the utilization of indicators for bacterial viability-such as the presence of specific transcripts or membrane integrity-would overcome bias introduced by cultivation and reduces the time span of analysis from initiation to read out. Therefore, we investigated the correlation between transcriptional activity, membrane integrity and cultivation-based viability in the Gram-positive model bacterium Bacillus subtilis.

Results

We present microbiological, cytological and molecular analyses of the physiological response to lethal heat stress under accurately defined conditions through systematic sampling of bacteria from a single culture exposed to gradually increasing temperatures. We identified a coherent transcriptional program including known heat shock responses as well as the rapid expression of a small number of sporulation and competence genes, the latter only known to be active in the stationary growth phase.

Conclusion

The observed coordinated gene expression continued even after cell death, in other words after all bacteria permanently lost their ability to reproduce. Transcription of a very limited number of genes correlated with cell viability under the applied killing regime. The transcripts of the expressed genes in living bacteria – but silent in dead bacteria-include those of essential genes encoding chaperones of the protein folding machinery and can serve as molecular biomarkers for bacterial cell viability.

Exploring Lactobacillus plantarum genome diversity by using microarrays

Lactobacillus plantarum is a versatile and flexible species that is encountered in a variety of niches and can utilize a broad range of fermentable carbon sources. To assess if this versatility is linked to a variable gene pool, microarrays containing a subset of small genomic fragments of L. plantarum strain WCFS1 were used to perform stringent genotyping of 20 strains of L. plantarum from various sources. The gene categories with the most genes conserved in all strains were those involved in biosynthesis or degradation of structural compounds like proteins, lipids, and DNA. Conversely, genes involved in sugar transport and catabolism were highly variable between strains. Moreover, besides the obvious regions of variance, like prophages, other regions varied between the strains, including regions encoding plantaricin biosynthesis, nonribosomal peptide biosynthesis, and exopolysaccharide biosynthesis. In many cases, these variable regions colocalized with regions of unusual base composition. Two large regions of flexibility were identified between 2.70 and 2.85 and 3.10 and 3.29 Mb of the WCFS1 chromosome, the latter being close to the origin of replication. The majority of genes encoded in these variable regions are involved in sugar metabolism. This functional overrepresentation and the unusual base composition of these regions led to the hypothesis that they represented lifestyle adaptation regions in L. plantarum. The present study consolidates this hypothesis by showing that there is a high degree of gene content variation among L. plantarum strains in genes located in these regions of the WCFS1 genome. Interestingly, based on our genotyping data L. plantarum strains clustered into two clearly distinguishable groups, which coincided with an earlier proposed subdivision of this species based on conventional methods.

Expression of heterologous genes in Schizophyllum commune is often hampered by the formation of truncated transcripts

GPD regulatory sequences were used to express a phleomycin resistance gene (Sh ble) in Schizophyllum commune, resulting in high numbers of phleomycin-resistant transformants. Attempts to express heterologous genes coding for hygromycin B phosphotransferase (hph), aminoglycoside phosphotransferase (apt), beta-glucuronidase (uidA) and beta-galactosidase (lacZ) using the same regulatory sequences were not successful and no mRNA could be detected. Cloning the hph and uidA genes in an internally deleted GPD gene resulted in truncated transcripts which ended within the 5'-parts of the heterologous genes. Cloning of the same genes as transcriptional fusions downstream from the Sh ble gene also resulted in truncated transcripts ending in the 5'-parts of these heterologous genes. It is suggested that AT-rich sequences in heterologous genes might be involved in generating these truncated transcripts, thereby preventing expression in S. commune.

Interfacial self-assembly of a hydrophobin into an amphipathic protein membrane mediates fungal attachment to hydrophobic surfaces

The SC3p hydrophobin of Schizophyllum commune is a small hydrophobic protein (100-101 amino acids with eight cysteine residues) that self-assembles at a water/air interface and coats aerial hyphae with an SDS-insoluble protein membrane, at the outer side highly hydrophobic and with a typical rodlet pattern. SC3p monomers in water also self-assemble at the interfaces between water and oils or hydrophobic solids. These materials are then coated with a 10 nm thick SDS-insoluble assemblage of SC3p making their surfaces hydrophilic. Hyphae of S. commune growing on a Teflon surface became firmly attached and SC3p was shown to be present between the fungal cell wall and the Teflon. Decreased attachment of hyphae to Teflon was observed in strains not expressing SC3, i.e. a strain containing a targeted mutation in this gene and a regulatory mutant thn. These findings indicate that hydrophobins, in addition to forming hydrophobic wall coatings, play a role in adherence of fungal hyphae to hydrophobic surfaces.

Highly-efficient transformation of the homobasidiomycete Schizophyllum commune to phleomycin resistance

Regulatory sequences of the glyceraldehyde-3-phosphate-dehydrogenase (GPD) gene from the homobasidiomycete Schizophyllum commune were fused to the coding sequence of the ble gene from Streptoalloteichus hindustanus, which codes for a phleomycin-binding protein. The resulting construct transformed S. commune to phleomycin resistance at a high frequency (up to 10(4) transformants/microgram DNA per 10(7) protoplasts) when regeneration was done in 0.5 M MgSO4. A similar construct with regulatory sequences from Aspergillus nidulans failed to give transformants, showing the importance of homologous regulatory sequences for the expression of genes in S. commune. The homologous GPD promoter could be deleted up to position -130 without any effect on the number of phleomycin-resistant transformants. This is the first effective stable transformation system in a homobasidiomycete employing antibiotic resistance.

The Sc7/Sc14 gene family of Schizophyllum commune codes for extracellular proteins specifically expressed during fruit-body formation

The Sc7 and Sc14 genes are specifically expressed in the dikaryon of the basidiomycete fungus Schizophyllum commune during fruiting. These genes are closely linked (within 6 kb) and highly similar in gene structure and nucleotide sequence (70% identical nucleotides in their coding regions). The encoded proteins (204 and 214 amino acids, respectively) have 87% similarity in amino acids (56% of the amino acids are identical). They contain putative signal sequences for secretion, are rich in aromatic amino acids which are generally located at similar positions, and they are generally hydrophilic. Inspection of databanks showed similarities with pathogenesis-related proteins (PR1) from plants, testis-specific proteins from mammals and venom allergen proteins from insects. An antibody raised against a Sc7 fusion protein showed the presence of the Sc7 protein in the culture medium and in the fruit bodies where it is apparently loosely associated with hyphal walls.

A homologous gene-reporter system for the basidiomycete Schizophyllum commune based on internally deleted homologous genes

Problems encountered in our attempts to achieve expression of heterologous genes, driven by ascomycetous regulatory sequences, in homobasidiomycetes led us to develop a gene-reporter system based on the expression of homologous genes in Schizophyllum commune. Internal deletions were made in the coding sequences of the regulated Sc4 gene and the constitutively expressed GPD gene. After introduction of these constructs into S. commune it was found that the expected truncated transcripts were produced. The internally deleted Sc4 gene, containing 1140bp of upstream and 200 bp of downstream sequences, was only expressed in dikaryons at the time of fruiting (as was the resident Sc4 gene) but not at all in monokaryons, indicating that the construct contained all regulatory sequences necessary and sufficient to confer control by the mating-type genes and expression during fruiting. The internally deleted GPD gene, containing 1300 bp of upstream and 150 bp of downstream sequences, was expressed both in monokaryons and dikaryons at levels similar to those of the resident GPD gene, indicating that all sequences necessary for proper expression were present. This reporter-gene system may be applicable to the analysis of cis-regulatory sequences of these genes. Furthermore, heterologous genes may be inserted into the well-expressed GPD deletion construct to obtain expression of such genes in S. commune and possibly in other homobasidiomycetes.

Sequence analysis of the glyceraldehyde-3-phosphate dehydrogenase genes from the basidiomycetes Schizophyllum commune, Phanerochaete chrysosporium and Agaricus bisporus

GPD genes encoding glyceraldehyde-3-phosphate dehydrogenase were isolated from the homobasidiomycetes Schizophyllum commune, Phanerochaete chrysosporium and Agaricus bisporus. All three species contain one transcriptionally active GPD gene, but A. bisporus also contains an inactive GPD gene (tandemly linked to the active gene). These genes contain 5-9 introns located at conserved positions, differing (except in one case) from intron positions in ascomycetous GPD genes. The predicted amino-acid sequences of the proteins encoded by the three active GPD genes are highly homologous. A comparison with protein sequences from filamentous ascomycetes shows a clear distinction, whereas the GPD genes from ascomycetous yeasts are quite distinct from both the filamentous ascomycetes and basidiomycetes. Promoter regions of ascomycetous GPD genes do not correspond to those of the GPD genes of basidiomycetes which may (partly) explain poor expression in basidiomycetes of introduced genes driven by an ascomycete GPD promoter.

Two genes specifically expressed in fruiting dikaryons of Schizophyllum commune: homologies with a gene not regulated by mating-type genes

The nucleotide (nt) sequences of the Sc3 and Sc4 genes of the filamentous fungus Schizophyllum commune, and the deduced amino acid (aa) sequences, were determined; moreover, the previously published sequence for the Sc1 gene [Dons et al., EMBO J. 3 (1984) 2101-2106] was corrected. All three independently isolated genes were found to have similar structures and nt sequences of their coding regions. At the aa level the homology is 43-62% (63-69% in the C-terminal parts of the proteins), the hydrophobic aa predominate and the hydrophobicity patterns are similar. All three proteins contain leader sequences and eight cysteines among about 110 aa, conserved at the same positions. Yet these genes are differentially regulated: Sc1 and Sc4 are only expressed at high levels in fruiting dikaryons, whereas Sc3 is highly expressed in both monokaryons and dikaryons, independent from fruiting.