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New Window Opens on the Secret Life of Microbes: Scientists Develop First Microbial Profiles of Ecosystems
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Archives of Microbiology (v.184, #3)
Cereulide-producing strains of Bacillus cereus show diversity by Camelia Apetroaie; Maria A. Andersson; Cathrin Spröer; Irina Tsitko; Ranad Shaheen; Elina L. Jääskeläinen; Luc M. Wijnands; Ritva Heikkilä; Mirja S. Salkinoja-Salonen (pp. 141-151).
Producers of cereulide, the emetic toxin of Bacillus cereus, are known to constitute a specific subset within this species. We investigated physiological and genetic properties of 24 strains of B. cereus including two high cereulide producers (600–1,800 ng cereulide mg−1 wet weight biomass), seven average producers (180–600 ng cereulide mg−1 wet weight biomass), four low cereulide producers (20–160 ng cereulide mg−1 wet weight biomass) and 11 non-producers representing isolates from food, food poisoning, human gut and environment. The 13 cereulide producers possessed 16S rRNA gene sequences identical to each other and identical to that of B. anthracis strains Ames, Sterne from GenBank and strain NC 08234–02, but showed diversity in the adk gene (two sequence types), in ribopatterns obtained with EcoRI and PvuII (three types of patterns), in tyrosin decomposition, haemolysis and lecithin hydrolysis (two phenotypes). The cereulide-producing isolates from the human gut represented two ribopatterns of which one was novel to cereulide-producing B. cereus and two phenotypes. We conclude that the cereulide-producing B. cereus are genetically and biochemically more diverse than hitherto thought.
Keywords: Cereulide; Bacillus cereus ; Ribopattern; 16S rRNA gene; Adk gene; Lecithinase; Haemolysis; Tyrosine decomposition
Cereulide-producing strains of Bacillus cereus show diversity by Camelia Apetroaie; Maria A. Andersson; Cathrin Spröer; Irina Tsitko; Ranad Shaheen; Elina L. Jääskeläinen; Luc M. Wijnands; Ritva Heikkilä; Mirja S. Salkinoja-Salonen (pp. 141-151).
Producers of cereulide, the emetic toxin of Bacillus cereus, are known to constitute a specific subset within this species. We investigated physiological and genetic properties of 24 strains of B. cereus including two high cereulide producers (600–1,800 ng cereulide mg−1 wet weight biomass), seven average producers (180–600 ng cereulide mg−1 wet weight biomass), four low cereulide producers (20–160 ng cereulide mg−1 wet weight biomass) and 11 non-producers representing isolates from food, food poisoning, human gut and environment. The 13 cereulide producers possessed 16S rRNA gene sequences identical to each other and identical to that of B. anthracis strains Ames, Sterne from GenBank and strain NC 08234–02, but showed diversity in the adk gene (two sequence types), in ribopatterns obtained with EcoRI and PvuII (three types of patterns), in tyrosin decomposition, haemolysis and lecithin hydrolysis (two phenotypes). The cereulide-producing isolates from the human gut represented two ribopatterns of which one was novel to cereulide-producing B. cereus and two phenotypes. We conclude that the cereulide-producing B. cereus are genetically and biochemically more diverse than hitherto thought.
Keywords: Cereulide; Bacillus cereus ; Ribopattern; 16S rRNA gene; Adk gene; Lecithinase; Haemolysis; Tyrosine decomposition
Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate by Steven Denkin; Sean Byrne; Charles Jie; Ying Zhang (pp. 152-157).
Salicylate stimulates the oxygen consumption and also induces multiple drug resistance in Mycobacterium tuberculosis. To gain insight into the mechanisms involved in the above observations, a microarray analysis of M. tuberculosis genes in response to salicylate was performed. Salicylate, besides highly inducing the 27 kD gene (Rv0560c) previously identified as highly salicylate-inducible, also caused increased transcription of a range of genes including an open reading frame (Rv0559c) that is located immediately downstream of the 27 kD gene, and some membrane/transmembrane proteins that may serve as potential efflux pumps or porins. Salicylate also caused a general shutdown of transcription and translation and energy production by down-regulating a range of genes involved in RNA and protein synthesis and ATP synthesis. The role of the salicylate-regulated genes in salicylate induced drug resistance and its unique effect on stimulating oxygen consumption in tubercle bacillus is discussed.
Keywords: Salicylate; Microarray; Gene regulation; Mycobacterium tuberculosis
Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate by Steven Denkin; Sean Byrne; Charles Jie; Ying Zhang (pp. 152-157).
Salicylate stimulates the oxygen consumption and also induces multiple drug resistance in Mycobacterium tuberculosis. To gain insight into the mechanisms involved in the above observations, a microarray analysis of M. tuberculosis genes in response to salicylate was performed. Salicylate, besides highly inducing the 27 kD gene (Rv0560c) previously identified as highly salicylate-inducible, also caused increased transcription of a range of genes including an open reading frame (Rv0559c) that is located immediately downstream of the 27 kD gene, and some membrane/transmembrane proteins that may serve as potential efflux pumps or porins. Salicylate also caused a general shutdown of transcription and translation and energy production by down-regulating a range of genes involved in RNA and protein synthesis and ATP synthesis. The role of the salicylate-regulated genes in salicylate induced drug resistance and its unique effect on stimulating oxygen consumption in tubercle bacillus is discussed.
Keywords: Salicylate; Microarray; Gene regulation; Mycobacterium tuberculosis
Biochemical characterization of trinitrotoluene transforming oxygen-insensitive nitroreductases from Clostridium acetobutylicum ATCC 824 by Razia Kutty; George N. Bennett (pp. 158-167).
The genes that encode oxygen-insensitive nitroreductases from Clostridium acetobutylicum possessing 2,4,6-Trinitrotoluene (TNT) transformation activity were cloned, sequenced and characterized. The gene products NitA (MW 31 kDa) and NitB (MW 23 kDa) were purified to homogeneity. The NitA and NitB are oxygen-insensitive nitroreductases comprised of a single nitroreductase domain. NitA and NitB enzymes show spectral characteristics similar to flavoproteins. The biochemical characteristics of NitA and NitB are highly similar to those of NfsA, the major nitroreductase from E. coli. NitA exhibited broad specificity similar to that of E. coli NfsA and displayed no flavin reductase activity. NitB showed broad substrate specificity toward nitrocompounds in a pattern similar to NfsA and NfsB of Escherichia coli. NitB has high sequence similarity to NAD(P)H nitroreductase from Archaeoglobus fulgidus. NitA could utilize only NADH as an electron donor, whereas NitB utilized both NADH and NADPH as electron donors with a preference for NADH. The activity of both nitroreductases was high toward 2,4-Dinitrotoluene (2,4-DNT) as a substrate. Both the nitroreductases were inhibited by dicoumarol and salicyl hydroxamate. The nitroreductases showed higher relative expression on induction with TNT, nitrofurazone and nitrofurantoin compared to the uninduced control.
Keywords: Oxygen-insensitive nitroreductase; Trinitrotoluene biotransformation; Flavoprotein
Biochemical characterization of trinitrotoluene transforming oxygen-insensitive nitroreductases from Clostridium acetobutylicum ATCC 824 by Razia Kutty; George N. Bennett (pp. 158-167).
The genes that encode oxygen-insensitive nitroreductases from Clostridium acetobutylicum possessing 2,4,6-Trinitrotoluene (TNT) transformation activity were cloned, sequenced and characterized. The gene products NitA (MW 31 kDa) and NitB (MW 23 kDa) were purified to homogeneity. The NitA and NitB are oxygen-insensitive nitroreductases comprised of a single nitroreductase domain. NitA and NitB enzymes show spectral characteristics similar to flavoproteins. The biochemical characteristics of NitA and NitB are highly similar to those of NfsA, the major nitroreductase from E. coli. NitA exhibited broad specificity similar to that of E. coli NfsA and displayed no flavin reductase activity. NitB showed broad substrate specificity toward nitrocompounds in a pattern similar to NfsA and NfsB of Escherichia coli. NitB has high sequence similarity to NAD(P)H nitroreductase from Archaeoglobus fulgidus. NitA could utilize only NADH as an electron donor, whereas NitB utilized both NADH and NADPH as electron donors with a preference for NADH. The activity of both nitroreductases was high toward 2,4-Dinitrotoluene (2,4-DNT) as a substrate. Both the nitroreductases were inhibited by dicoumarol and salicyl hydroxamate. The nitroreductases showed higher relative expression on induction with TNT, nitrofurazone and nitrofurantoin compared to the uninduced control.
Keywords: Oxygen-insensitive nitroreductase; Trinitrotoluene biotransformation; Flavoprotein
Amino acid variation in cellular processes in 108 bacterial proteomes by Devarajan Bharanidharan; Namasivayam Gautham (pp. 168-174).
We have analysed 108 bacterial proteomes in the KEGG database to explore the variation of amino acid composition with respect to protein function. The ratio between the observed amino acid composition and that predicted based on mononucleotide composition was calculated for each functional category. This indicated whether the compositional variation arose from mutation or selection pressure. The results showed that charged amino acids (Lys, Arg and Glu), were found more frequently than expected in proteins involved in genetic information processing (i.e. transcription, translation, etc.) Similarly, in the proteins involved in processing environmental information (e.g. signal transduction), the hydrophobic amino acid Leu was found in excess of values expected from the base composition in the genes.
Keywords: Amino acid composition; Nucleotide bias; Functional category; Hydropathy index
Amino acid variation in cellular processes in 108 bacterial proteomes by Devarajan Bharanidharan; Namasivayam Gautham (pp. 168-174).
We have analysed 108 bacterial proteomes in the KEGG database to explore the variation of amino acid composition with respect to protein function. The ratio between the observed amino acid composition and that predicted based on mononucleotide composition was calculated for each functional category. This indicated whether the compositional variation arose from mutation or selection pressure. The results showed that charged amino acids (Lys, Arg and Glu), were found more frequently than expected in proteins involved in genetic information processing (i.e. transcription, translation, etc.) Similarly, in the proteins involved in processing environmental information (e.g. signal transduction), the hydrophobic amino acid Leu was found in excess of values expected from the base composition in the genes.
Keywords: Amino acid composition; Nucleotide bias; Functional category; Hydropathy index
Occurrence and regulation of the ferric citrate transport system in Escherichia coli B, Klebsiella pneumoniae, Enterobacter aerogenes, and Photorhabdus luminescens by Susanne Mahren; Heidrun Schnell; Volkmar Braun (pp. 175-186).
In Escherichia coli K-12, transcription of the ferric citrate transport genes fecABCDE is initiated by binding of diferric dicitrate to the outer membrane protein FecA which elicits a signaling cascade from the cell surface to the cytoplasm. The FecI sigma factor is only active in the presence of FecR, which transfers the signal across the cytoplasmic membrane. In other bacteria, fecIRA homologues control iron transport gene transcription by siderophores other than citrate. However, in most cases, the FecI homologues are active in the absence of the FecR homologues, which might function as anti-sigma factors. Since not all E. coli strains contain a fec system, we determined the occurrence of fec genes in selected Enterobacteriaceae and the dependence of FecI activity on FecR. Incomplete FecIRA systems were chromosomally encoded in Enterobacter aerogenes strains and plasmid-encoded in K. pneumoniae. E. coli B, Photorhabdus luminescens and one of three Klebsiella pneumoniae strains had a functional FecIRA regulatory system as in E. coli K-12. The cytoplasmic N-terminal FecR fragments caused constitutive FecI activity in the absence of ferric citrate. The PCR-generated mutant FecI(D40G) was inactive and FecI(S15P) was partially active. FecR of E. coli K-12 activated FecI of all tested strains except FecI encoded on the virulence plasmid pLVPK of K. pneumoniae, which differed from E. coli K-12 FecI by having mutations in region 4, which is important for interaction with FecR. The C-terminally truncated FecR homologue of pLVPK was inactive. pLVPK-encoded FecA contains a 38-residue sequence in front of the signal sequence that did not prevent processing and proper integration of FecA into the outer membrane of E. coli and lacks the signaling sequence required for transcription initiation of the fec transport genes, making it induction-incompetent but transport-competent. The evidence indicates that fecIRABCDE genes are acquired by horizontal DNA transfer and can undergo debilitating mutations.
Keywords: FecIRA; Transmembrane transcription control; Surface signaling; Escherichia coli B; Klebsiella pneumoniae ; Enterobacter aerogenes ; Photorhabdus luminescens ; Virulence plasmid
Occurrence and regulation of the ferric citrate transport system in Escherichia coli B, Klebsiella pneumoniae, Enterobacter aerogenes, and Photorhabdus luminescens by Susanne Mahren; Heidrun Schnell; Volkmar Braun (pp. 175-186).
In Escherichia coli K-12, transcription of the ferric citrate transport genes fecABCDE is initiated by binding of diferric dicitrate to the outer membrane protein FecA which elicits a signaling cascade from the cell surface to the cytoplasm. The FecI sigma factor is only active in the presence of FecR, which transfers the signal across the cytoplasmic membrane. In other bacteria, fecIRA homologues control iron transport gene transcription by siderophores other than citrate. However, in most cases, the FecI homologues are active in the absence of the FecR homologues, which might function as anti-sigma factors. Since not all E. coli strains contain a fec system, we determined the occurrence of fec genes in selected Enterobacteriaceae and the dependence of FecI activity on FecR. Incomplete FecIRA systems were chromosomally encoded in Enterobacter aerogenes strains and plasmid-encoded in K. pneumoniae. E. coli B, Photorhabdus luminescens and one of three Klebsiella pneumoniae strains had a functional FecIRA regulatory system as in E. coli K-12. The cytoplasmic N-terminal FecR fragments caused constitutive FecI activity in the absence of ferric citrate. The PCR-generated mutant FecI(D40G) was inactive and FecI(S15P) was partially active. FecR of E. coli K-12 activated FecI of all tested strains except FecI encoded on the virulence plasmid pLVPK of K. pneumoniae, which differed from E. coli K-12 FecI by having mutations in region 4, which is important for interaction with FecR. The C-terminally truncated FecR homologue of pLVPK was inactive. pLVPK-encoded FecA contains a 38-residue sequence in front of the signal sequence that did not prevent processing and proper integration of FecA into the outer membrane of E. coli and lacks the signaling sequence required for transcription initiation of the fec transport genes, making it induction-incompetent but transport-competent. The evidence indicates that fecIRABCDE genes are acquired by horizontal DNA transfer and can undergo debilitating mutations.
Keywords: FecIRA; Transmembrane transcription control; Surface signaling; Escherichia coli B; Klebsiella pneumoniae ; Enterobacter aerogenes ; Photorhabdus luminescens ; Virulence plasmid
Production of volatile organic compounds (VOCs) by yeasts isolated from the ascocarps of black (Tuber melanosporum Vitt.) and white (Tuber magnatum Pico) truffles by Pietro Buzzini; Chiara Gasparetti; Benedetta Turchetti; Maria Rita Cramarossa; Ann Vaughan-Martini; Alessandro Martini; Ugo Maria Pagnoni; Luca Forti (pp. 187-193).
Twenty-nine yeast strains were isolated from the ascocarps of black and white truffles (Tuber melanosporum Vitt. and Tuber magnatum Pico, respectively), and identified using a polyphasic approach. According to the conventional taxonomic methods, MSP-PCR fingerprinting and sequencing of the D1/D2 domain of 26S rDNA, the strains were identified as Candida saitoana, Debaryomyces hansenii, Cryptococcus sp., Rhodotorula mucilaginosa, and Trichosporon moniliiforme. All isolates assimilated l-methionine as a sole nitrogen source and produced the volatile organic compounds (VOCs), 2-methyl butanol, 3-methyl butanol, methanethiol, S-methyl thioacetate, dimethyl sulfide, dimethyl disulfide, dimethyl trisulfide, dihydro-2-methyl-3(2H)-thiophenone and 3-(methylthio)-1-propanol (MTP). ANOVA analysis of data showed significant (P<0.01) differences in VOCs produced by different yeasts, with MTP as the major component (produced at concentrations ranging from 19.8 to 225.6 mg/l). In addition, since some molecules produced by the isolates of this study are also characteristic of truffle complex aroma, it is possible to hypothesize a complementary role of yeasts associated with this ecosystem in contributing to final Tuber spp. aroma through the independent synthesis of yeast-specific volatile constituents.
Keywords: VOC producing yeasts; Black and white truffles; Aroma; Tuber melanosporum Vitt.; Tuber magnatum Pico
Production of volatile organic compounds (VOCs) by yeasts isolated from the ascocarps of black (Tuber melanosporum Vitt.) and white (Tuber magnatum Pico) truffles by Pietro Buzzini; Chiara Gasparetti; Benedetta Turchetti; Maria Rita Cramarossa; Ann Vaughan-Martini; Alessandro Martini; Ugo Maria Pagnoni; Luca Forti (pp. 187-193).
Twenty-nine yeast strains were isolated from the ascocarps of black and white truffles (Tuber melanosporum Vitt. and Tuber magnatum Pico, respectively), and identified using a polyphasic approach. According to the conventional taxonomic methods, MSP-PCR fingerprinting and sequencing of the D1/D2 domain of 26S rDNA, the strains were identified as Candida saitoana, Debaryomyces hansenii, Cryptococcus sp., Rhodotorula mucilaginosa, and Trichosporon moniliiforme. All isolates assimilated l-methionine as a sole nitrogen source and produced the volatile organic compounds (VOCs), 2-methyl butanol, 3-methyl butanol, methanethiol, S-methyl thioacetate, dimethyl sulfide, dimethyl disulfide, dimethyl trisulfide, dihydro-2-methyl-3(2H)-thiophenone and 3-(methylthio)-1-propanol (MTP). ANOVA analysis of data showed significant (P<0.01) differences in VOCs produced by different yeasts, with MTP as the major component (produced at concentrations ranging from 19.8 to 225.6 mg/l). In addition, since some molecules produced by the isolates of this study are also characteristic of truffle complex aroma, it is possible to hypothesize a complementary role of yeasts associated with this ecosystem in contributing to final Tuber spp. aroma through the independent synthesis of yeast-specific volatile constituents.
Keywords: VOC producing yeasts; Black and white truffles; Aroma; Tuber melanosporum Vitt.; Tuber magnatum Pico
Production and partial characterization of extracellular proteinases from Streptomyces malaysiensis, isolated from a Brazilian cerrado soil by Rodrigo P. Nascimento; Claudia M. d’Avila-Levy; Rodrigo F. Souza; Marta H. Branquinha; Elba P. S. Bon; Nei Pereira-Jr; Rosalie R. R. Coelho (pp. 194-198).
Streptomyces malaysiensis AMT-3, isolated from a Brazilian cerrado soil, showed proteolytic activities detected by gelatin–sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The optimum proteinase production was obtained when using 2.5% wheat bran and 0.1% yeast extract in the culture medium, after 5 days incubation at 30°C. The enzymatic complex degraded gelatin optimally at pH 7.0, and under these conditions eight proteolytic bands (four serine-proteinases and four metaloproteinases), ranging from 20 to 212 kDa, were detected on the culture supernatant filtrates. In addition, a 35-kDa proteinase was thermostable at 60°C for 120 min. These results point out to the applicability of gelatin zymograms in the characterization of crude enzymatic complexes. According to our results, this enzymatic complex could be used for biotechnological applications.
Keywords: Streptomyces malaysiensis ; Thermostable proteinase; Enzyme characterization; Wheat bran
Production and partial characterization of extracellular proteinases from Streptomyces malaysiensis, isolated from a Brazilian cerrado soil by Rodrigo P. Nascimento; Claudia M. d’Avila-Levy; Rodrigo F. Souza; Marta H. Branquinha; Elba P. S. Bon; Nei Pereira-Jr; Rosalie R. R. Coelho (pp. 194-198).
Streptomyces malaysiensis AMT-3, isolated from a Brazilian cerrado soil, showed proteolytic activities detected by gelatin–sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The optimum proteinase production was obtained when using 2.5% wheat bran and 0.1% yeast extract in the culture medium, after 5 days incubation at 30°C. The enzymatic complex degraded gelatin optimally at pH 7.0, and under these conditions eight proteolytic bands (four serine-proteinases and four metaloproteinases), ranging from 20 to 212 kDa, were detected on the culture supernatant filtrates. In addition, a 35-kDa proteinase was thermostable at 60°C for 120 min. These results point out to the applicability of gelatin zymograms in the characterization of crude enzymatic complexes. According to our results, this enzymatic complex could be used for biotechnological applications.
Keywords: Streptomyces malaysiensis ; Thermostable proteinase; Enzyme characterization; Wheat bran