Investigations on the microbial catabolism of the organic sulfur compounds TDP and DTDP in Ralstonia eutropha H16 employing DNA microarrays

In this study, we have investigated the transcriptome of Ralstonia eutropha H16 during cultivation with gluconate in presence of 3,3′-thiodipropionic acid (TDP) or 3,3′-dithiodipropionic acid (DTDP) during biosynthesis of poly(3-hydroxybutyrate-co-3-mercaptopropionate). Genome-wide transcriptome analyses revealed several genes which were upregulated during cultivation in presence of the above-mentioned compounds. Obtained data strongly suggest that two ABC-type transport system and three probable extracytoplasmic solute receptors mediate the uptake of TDP and DTDP, respectively. In addition, genes encoding the hydrolase S-adenosylhomocysteinase AhcY and the thiol-disulfide interchange proteins DsbA, DsbD, and FrnE were upregulated during cultivation on DTDP and, in case of AhcY and FrnE, on TDP as well. It is assumed that the corresponding enzymes are involved in the cleavage of TDP and DTDP. Several genes of the fatty acid metabolism exhibited increased expression levels: genes encoding two acetyltransferases, a predicted acyltransferase, the acetoacetyl-CoA reductase phaB3, an enoyl-CoA hydratase as well as an acyl dehydratase, an acetyl-CoA synthetase, two acyl-CoA dehydrogenases, the methylmalonyl-CoA mutase encoded by sbm1 and sbm2 and phaY1 were detected. Furthermore, ORF H16_A0217 encoding a hypothetical protein and exhibiting 54% amino acids identical to an acyl-CoA thioesterase from Saccharomonospora viridis was found to be highly upregulated. As the 2-methylcitrate synthase PrpC exhibited a three- to fourfold increased activity in cells grown in presence of TDP or DTDP as compared to gluconate, metabolization of the cleavage products 3MP and 3-hydroxypropionate to propionyl-CoA is proposed

Phenotypic and transcriptomic analyses of seven clinical Stenotrophomonas maltophilia isolates identify a small set of shared and commonly regulated genes involved in the biofilm lifestyle

Stenotrophomonas maltophilia is one of the most frequently isolated multidrug-resistant nosocomial opportunistic pathogens. It contributes to disease progression in cystic fibrosis (CF) patients and is frequently isolated from wounds, infected tissues, and catheter surfaces. On these diverse surfaces S. maltophilia lives in single-species or multispecies biofilms. Since very little is known about common processes in biofilms of different S. maltophilia isolates, we analyzed the biofilm profiles of 300 clinical and environmental isolates from Europe of the recently identified main lineages Sgn3, Sgn4, and Sm2 to Sm18. The analysis of the biofilm architecture of 40 clinical isolates revealed the presence of multicellular structures and high phenotypic variability at a strain-specific level. Further, transcriptome analyses of biofilm cells of seven clinical isolates identified a set of 106 shared strongly expressed genes and 33 strain-specifically expressed genes. Surprisingly, the transcriptome profiles of biofilm versus planktonic cells revealed that just 9.43% ± 1.36% of all genes were differentially regulated. This implies that just a small set of shared and commonly regulated genes is involved in the biofilm lifestyle. Strikingly, iron uptake appears to be a key factor involved in this metabolic shift. Further, metabolic analyses implied that S. maltophilia employs a mostly fermentative growth mode under biofilm conditions. The transcriptome data of this study together with the phenotypic and metabolic analyses represent so far the largest data set on S. maltophilia biofilm versus planktonic cells. This study will lay the foundation for the identification of strategies for fighting S. maltophilia biofilms in clinical and industrial settings. IMPORTANCE Microorganisms living in a biofilm are much more tolerant to antibiotics and antimicrobial substances than planktonic cells are. Thus, the treatment of infections caused by microorganisms living in biofilms is extremely difficult. Nosocomial infections (among others) caused by S. maltophilia, particularly lung infection among CF patients, have increased in prevalence in recent years. The intrinsic multidrug resistance of S. maltophilia and the increased tolerance to antimicrobial agents of its biofilm cells make the treatment of S. maltophilia infection difficult. The significance of our research is based on understanding the common mechanisms involved in biofilm formation of different S. maltophilia isolates, understanding the diversity of biofilm architectures among strains of this species, and identifying the differently regulated processes in biofilm versus planktonic cells. These results will lay the foundation for the treatment of S. maltophilia biofilms

Phage vB_BveM-Goe7 represents a new genus in the subfamily Bastillevirinae

Bacillus velezensis FZB42 is a Gram-positive, endospore-forming rhizobacterium that is associated with plant roots and promotes plant growth. It was used as host to isolate phage vB_BveM-Goe7 (Goe7). Goe7 exhibits a Myoviridae morphology with a contractile tail and an icosahedral head. Its genome is 158,674 bp in size and contains 5137-bp-long terminal repeats (LTRs). It also contains five tRNA-encoding genes and 251 coding DNA sequences (CDS), of which 65 were annotated. The adsorption constant of Goe7 is 6.1 ± 0.24 × 10⁻⁸ ml/min, with a latency period of 75 min and a burst size of 114 particles per burst. A BLASTn sequence comparison against the non-redundant nucleotide database of NCBI revealed that Goe7 is most similar to Bacillus subtilis phage vB_BsuM-Goe3

Genome-based metabolic and phylogenomic analysis of three Terrisporobacter species.

Acetogenic bacteria are of high interest for biotechnological applications as industrial platform organisms, however, acetogenic strains from the genus Terrisporobacter have hitherto been neglected. To date, three published type strains of the genus Terrisporobacter are only covered by draft genome sequences, and the genes and pathway responsible for acetogenesis have not been analyzed. Here, we report complete genome sequences of the bacterial type strains Terrisporobacter petrolearius JCM 19845T, Terrisporobacter mayombei DSM 6539T and Terrisporobacter glycolicus DSM 1288T. Functional annotation, KEGG pathway module reconstructions and screening for virulence factors were performed. Various species-specific vitamin, cofactor and amino acid auxotrophies were identified and a model for acetogenesis of Terrisporobacter was constructed. The complete genomes harbored a gene cluster for the reductive proline-dependent branch of the Stickland reaction located on an approximately 21 kb plasmid, which is exclusively found in the Terrisporobacter genus. Phylogenomic analysis of available Terrisporobacter genomes suggested a reclassification of most isolates as T. glycolicus into T. petrolearius

Comparison of the circular plasmids in the three <i>Terrisporobacter</i> type strains.

The plasmids encode a proline-dependent gene cluster for the reductive branch of the Stickland reaction. The legend for the size and the sequence identity of translated genes is shown at the bottom in kilobases (kb) and from 0% (white) to 100% (black). The following genes are encoded: selC, tRNA-Sec; prdD, proline reductase cluster protein PrdD; prdE; proline reductase cluster protein PrdE; csd, putative cysteine desulfurase; lysR, lysR family transcriptional regulator; selB, selenocysteine-specific elongation factor; selA, L-seryl-tRNA (Sec) selenium transferase; selD, selenide water dikinase; parA, parA family protein; hin, DNA-invertase; csp, cold shock protein; parB, DNA primase; prdB, D-proline reductase subunit gamma; prdA, D-proline reductase proprotein PrdA; prdC, proline reductase-associated electron transfer protein; hyp, hypothetical protein.</p

Reconstruction of the Wood-Ljungdahl pathway in <i>Terrisporobacter</i>.

A: Genome-based reconstruction of the Wood-Ljungdahl pathway for the three type strains of the Terrisporobacter genus. Genome locus tags (black) of the catalyzing enzymes (red) and the required genes (blue) are shown for the three type strains of the Terrisporobacter genus (TEMA, T. mayombei DSM 6539T; TEPE, T. petrolearius JCM 19845T; TEGL, T. glycolicus DSM 1288T). B: Genomic organization of the HDCR-complex gene cluster in the three Terrisporobacter type strains in comparison to the type strain of C. difficile DSM 1269T. The following gene abbreviations were used: fdhF, formate dehydrogenase H; hyfA, hydrogenase-4 component A; hndD, NADP-reducing hydrogenase; focA, putative formate transporter; fdhD, sulfur carrier protein. C: Genomic organization of the Wood-Ljungdahl gene cluster in the three Terrisporobacter type strains in comparison to the type strain of C. difficile DSM 1269T. The following gene abbreviations were used: acsA, anaerobic carbon-monoxide dehydrogenase catalytic subunit; acsF, carbon monoxide dehydrogenase accessory protein; fhs, formyl THF synthetase; fchA, methenyl THF cyclohydrolase; folD, bifunctional cyclohydrolase/dehydrogenase; metV, methylene THF reductase C-terminal catalytic subunit; metF, methylene THF reductase large subunit; lpdA, dihydrolipoyl dehydrogenase; cooC, carbon monoxide dehydrogenase accessory protein; acsD, CoFeSP small subunit; acsC, CoFeSP large subunit; acsE, methyl THF CoFeSP methyltransferase; acsB, carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta; gcvH, glycine cleavage system H protein; acsV, corrinoid activation/regeneration protein. The following enzyme abbreviations were used: HDCR, hydrogen-dependent CO2 reductase; FTS, formyl-THF synthetase; MTC, methenyl-THF cyclohydrolase; MTD, methylene-THF dehydrogenase; MTR, methylene-THF reductase; MT, methyl-transferase; CODH, carbon monoxide dehydrogenase; ACS, acetyl-CoA synthetase; PTA, phosphotransacetylase, ACK, acetate kinase. The legend for size and sequence identity of translated genes are shown at the bottom of B and C in kilobases (kb) and from 0% (white) to 100% (black).</p

Phylogenomic analysis of <i>Terrisporobacter</i> genome sequences.

The legend for sequence identities is shown in the top left corner. Sequence identities higher than 95% are shown in red, while lower values are colored grey to blue. The three type strains of the genomes sequenced from the Terrisporobacter genus in this study are highlighted in green. Genome sequences derived from metagenomic assemblies are indicated by MAG in parentheses.</p

Functional annotation and pan/core genome analysis.

A Functional annotation of the Terrisporobacter type strain genomes into COG categories. The y-axis shows the different COG categories and the x-axis the number of genes assigned to each category by eggNOG-mapper. The bar color indicates the number of genes for the three Terrisporobacter type strains T. mayombei (green), T. petrolearius (blue) and T. glycolicus (red). B Pan/core genome analysis of three Terrisporobacter type strains. The Venn diagram visualizes the exclusive and shared gene clusters for T. mayombei (green), T. petrolearius (blue) and T. glycolicus (red) created with OrthoVenn2. The graph visualizes the total number of gene clusters in the three genomes using the same color code.</p