Deoxyribonuclease activity in rumen bacteria

Heterologous gene expression in the human gut bacteria Eubacterium rectale and Roseburia inulinivorans by means of conjugative plasmids

Commensal butyrate-producing bacteria in the Firmicutes phylum are abundant in the human intestine and are important for maintaining health. However, understanding of the metabolism and host interaction of these bacteria is limited by the lack of genetic modification techniques. Here we establish a protocol enabling the transfer of autonomously-replicating shuttle vectors by conjugative plasmid transfer from an Escherichia coli donor into representatives of an important sub-group of strictly anaerobic human colonic Firmicutes. Five different plasmid shuttle vectors were tested, each carrying a different origin of replication from Gram-positive bacteria. Plasmid pMTL83151 (pCB102 replicon) were successfully transferred into two strains of Eubacterium rectale, while pMTL83151 and pMTL82151 (pBP1 replicon) were transferred into Roseburia inulinivorans A2-194. Plasmids that carried a Streptococcus bovis JB1 glycoside hydrolase family 16 β-(1,3-1,4)-glucanase gene were constructed and conjugated into Roseburia inulinivorans A2-194 and Eubacterium rectale T1-815, resulting in successful heterologous expression of this introduced enzymatic activity in these two strains of butyrate-producing Firmicutes.

Composting: A Potentially Safe Process for Disposal of Genetically Modified Organisms

The widespread use of genetically modified organisms (GMOs) may result in the release of GMOs into the environment. The potential risks regarding their use and implementation of disposal methods, especially the possibility of novel genes from GMOs being transferred to natural organisms, need to be evaluated and better understood. There is an increasingly accepted public view that GMO products introduced into the environment should be degradable and should disappear after a limited period of time. Due to the risk of possible horizontal gene transfer, disposal methods for GMOs need to address destruction of both the organism and the genetic material. During the last two decades, we have developed a greater understanding of the biochemical, microbiological and molecular concepts of the composting process, such that maximum decomposition may be achieved in the shortest time with minimal negative impacts to the environment. The conditions created in a properly managed composting process environment may help in destroying GMOs and their genes, thereby reducing the risk of the spread of genetic material. When considering composting as a potential method for the disposal of GMOs, the establishment of controlled conditions providing an essentially homogenous environment appears to be an important requirement. An evaluation of composting as a safe option for disposal of GMOs is provided in this review.

Expression of nuclease gene nucA, a member of an operon putatively involved in uracil removal from DNA and its subsequent reuse in Prevotella bryantii

The genomic region of Prevotella bryantii TC1-1 that conferred an increased nucleolytic activity on Escherichia coli was characterized. It contains two divergent transcriptional units separated by an AT-rich promoter region. One unit is comprised of three genes involved in nucleotide metabolism. nucA, the first gene of this unit, whose product belongs to exonuclease/endonuclease/phosphatase Pfam family, was thought to be required for the increased nucleolytic activity and various expression strategies were employed to confirm its role. The nucA expression was only successful in cell free system where DNase and RNase activity was observed. Two genes downstream of nucA code for a putative uracil DNA glycosylase and uridine kinase which could be involved in the removal of misincorporated uracil from DNA and its reuse. Given that apurinic/apyrimidinic nuclease activity is required after uracil removal from DNA, it was somewhat surprising to find out that nucA, whose product belongs to protein family consisting mostly of apurinic/apyrimidinic nucleases, has no apurinic/apyrimidinic activity.

Conventional and real-time polymerase chain reaction assessment of the fate of transgenic DNA in sheep fed Roundup Ready rapeseed meal

Conventional and real-time PCR were used to detect transgenic DNA in digesta, faeces and blood collected from six ruminally and duodenally cannulated sheep fed forage-based (F) or concentrate-based (C) diets containing 15% Roundup Ready (RR) rapeseed meal (n 3). The sheep were adapted for 14 d to F or C diets containing non-GM rapeseed, then fed the RR diets for 11 d. On day 12, they were switched back to non-GM diets for a further 11 d. Ruminal and duodenal fluids (RF, DF) and faecal samples were collected at 3 or 4 h intervals over the 4 d immediately following the last feeding of GM diets. DNA was isolated from whole RF and DF, from the cell-free supernatant fraction, and from culture fermentation liquid. Blood was collected on days 1, 5 and 9 of feeding the RR rapeseed meal. The 1363 bp 5-enolpyruvylshikimate-3-phosphate synthase transgene (epsps) was quantifiable in whole RF and DF for up to 13 h, and a 108 bp epsps fragment for up to 29 h. Transgenic DNA was not detectable in faeces or blood, or in microbial DNA. Diet type (F v. C) did not affect (P>0.05) the quantity of transgenic DNA in digesta. More (P<0.05) transgenic DNA was detected in RF than in DF, but there was an interaction (P<0.05) between sample type and collection time. In supernatant fractions from RF and DF, three different fragments of transgenic DNA ranging in size from 62 to 420 bp were not amplifiable.

Improved extraction of PCR-quality community DNA from digesta and fecal samples

Several DNA extraction methods have been reported for use with digesta or fecal samples, but problems are often encountered in terms of relatively low DNA yields and/or recovering DNA free of inhibitory substances. Here we report a modified method to extract PCR-quality microbial community DNA from these types of samples, which employs bead beating in the presence of high concentrations of sodium dodecyl sulfate (SDS), salt, and EDTA, and with subsequent DNA purification by QIAamp columns [referred to as repeated bead beating plus column (RBB + C) method]. The RBB + C method resulted in a 1.5- to 6-fold increase in DNA yield when compared to three other widely used methods. The community DNA prepared with the RBB + C method was also free of inhibitory substances and resulted in improved denaturing gradient gel electrophoresis (DGGE) profiles, which is indicative of a more complete lysis and representation of microbial diversity present in such samples.

Use of quantitative real-time and conventional PCR to assess the stability of the cp4 epsps transgene from Roundup Ready canola in the intestinal, ruminal, and fecal contents of sheep

The stability of transgenic DNA encoding the synthetic cp4 epsps protein in a diet containing Roundup Ready (RR) canola meal was determined in duodenal fluid (DF) batch cultures from sheep. A real-time TaqMan PCR assay was designed to quantify the degradation of cp4 epsps DNA during incubation in DF at pH 5 or 7. The copy number of cp4 epsps DNA in the diet declined more rapidly (P < 0.05) in DF at pH 5 as compared to pH 7. The decrease was attributed mainly to microbial activity at pH 7 and perhaps to plant endogenous enzymes at pH 5. The 62-bp fragment of cp4 epsps DNA detected by real-time PCR reached a maximum of approximately 1600 copies in the aqueous phase of DF at pH 7, whereas less than 20 copies were detected during incubations in DF at pH 5. A 1363-bp sequence of cp4 epsps DNA was never detected in the aqueous fraction of DF. Additionally, genomic DNA isolated from RR canola seed was used to test the persistence of fragments of free DNA in DF at pH 3.2, 5, and 7, as well as in ruminal fluid and feces. Primers spanning the cp4 epsps DNA coding region amplified sequences ranging in size from 300 to 1363 bp. Free transgenic DNA was least stable in DF at pH 7 where fragments less than 527 bp were detected for up to 2 min and fragments as large as 1363 bp were detected for 0.5 min. This study shows that digestion of plant material and release of transgenic DNA can occur in the ovine small intestine. However, free DNA is rapidly degraded at neutral pH in DF, thus reducing the likelihood that intact transgenic DNA would be available for absorption through the Peyer's Patches in the distal ileum.

Molecular microbiology of gut bacteria: genetic diversity and community structure analysis

Recently developed molecular biology approaches make possible the detailed genetic, taxonomic and ecological examination of microorganisms from various habitats. Animal gut represents one of the most complex microbial ecosystems with a large degree of microbial biodiversity present. Bacteria inhabiting the gut usually play important roles in metabolic transformations of substrates and sometimes, e.g. in ruminants, they make the basis for an obligate symbiosis with the host. Here we discuss molecular microbiology as a strategy for examination of gut bacteria, concentrating on a typical and in such environment dominant group of strictly anaerobic Gram-negative bacteria from the phylogenetic group Cytophaga/Flexibacter/Bacteroides. The bacteria from the genus Prevotella are the most abundant Gram-negative bacteria in the rumen and form a distinctive phylogenetic cluster, clearly separated from prevotellas isolated from other ecological niches. They may represent a good choice for a model organism in genetic manipulation experiments and for studies of gene transfer mechanisms taking place in the gut. The molecular tools for detection and monitoring of ruminal prevotellas are discussed.

Is Pseudobutyrivibrio xylanivorans strain Mz5T suitable as a probiotic? An in vitro study

Rumen bacterium Pseudobutyrivibrio xylanivorans strain Mz5T possessed a potent xylanolytic enzyme system consisting of at least 7 different xylan hydrolases with molar mass 27-145 kDa. Three of them were successfully isolated in active native form. This strain produced butyrate and lactate on different saccharides. cis-9, trans-11-Conjugated linoleic acid was also detected in the culture medium. Bacteriocin-like inhibitory substances of Mz5T were active against some strains of rumen bacteria and against selected Salmonella and E. coli isolates from poultry meat. The strain Mz5T retained viability and xylanolytic activity also under not fully anaerobic conditions; its cells attached to the Caco-2 cells so that its successful association with gut epithelial cells may be expected. These in vitro results confirmed several probiotic traits of the isolate Mz5T and justified further in vivo experiments to test its ability to improve animal health and performance.

Impact of feed processing and mixed ruminal culture on the fate of recombinant EPSP synthase and endogenous canola plant DNA

The impact of feed processing and in vitro ruminal cultures on the persistence of recombinant and canola-specific endogenous DNA was studied using various canola substrates (whole seed, cracked seed, meal and diet). For both, parental and genetically modified substrates, ribulose-1,5-bisphosphate carboxylase/oxygenase gene was amplifiable up to varying time points. Persistence of recombinant DNA, encoding 5-enolpyruvylshikimate-3-phosphate synthase (1,363 bp) was detected up to 8 h for meal and 4 h for mixed diet. Upon processing of canola, DNA large enough to contain intact plant genes remains. In an in vitro environment, plant DNA was rapidly degraded upon its release into rumen fluid.

Potential for the environmental impact of transgenic crops

In recent years, there has been increasing interest in how changes in agricultural practice associated with the introduction of particular genetically modified (GM) crops might indirectly impact the environment. There is also interest in any effects that might be associated with recombinant and novel combinations of DNA passing into the environment, and the possibility that they may be taken up by microorganisms or other live biological material. From the current state of knowledge, the impact of free DNA of transgenic origin is likely to be negligible compared with the large amount of total free DNA. We can find no compelling scientific arguments to demonstrate that GM crops are innately different from non-GM crops. The kinds of potential impacts of GM crops fall into classes familiar from the cultivation of non-GM crops (e.g., invasiveness, weediness, toxicity, or biodiversity). It is likely, however, that the novelty of some of the products of GM crop improvement will present new challenges and perhaps opportunities to manage particular crops in creative ways.

The bacteriophages of ruminal prevotellas

Rumen bacteriophage-lyzed bacterial strains of the genus Prevotella were isolated and preliminarily characterized. The strain TCl-1 the species P. bryantii was the only prevotella strain successfully infected with filter sterilized rumen fluid from a black-and-white Holstein cow. Two types of plaques were observed, both rather small and turbid. Preliminary electron microscopy observation showed that several morphologically different bacteriophages were present in these plaques. The plaque eluates were further used for the infection of other prevotella strains. The plaques produced by the bacteriophages were observed with two strains, i.e. P. bryantii B(1)4 and P. brevis GA33. The bacteriophages from both strains were examined by transmission electron microscopy and several morphologically different bacteriophages were observed, among others also a large virion with an icosahedral head with the diameter of approximately 120 nm. The bacteriophage was identified in plaques of bacterial cells of the strain GA33 and has an approximately 800 nm long helical tail, which places it among the largest ruminal bacteriophages described to date. Other bacteriophages from the same indicator strain as well as from P. bryantii B(1)4 strain were smaller and tail structures were not observed in all of them.

Non-specific DNAases from the rumen bacterium Prevotella bryantii

Extracellular non-specific nucleases were observed in some strains belonging to the ruminal species of the genus Prevotella, mostly P. brevis and P. bryantii. The nuclease from P. bryantii appeared to be extracellular; it mediates the degradation of the supercoiled plasmid DNA via an open circle intermediate. The cleavage is not site specific although a preference for certain cleavage sites does seem to exist. Our attempts to clone the wild-type P. bryantii B(1)4 nuclease in E. coli strain ER1992 that reports on the DNA damage sustained, were unsuccessful probably due to excessive intracellular nuclease activity that killed the cells bearing the gene for the nuclease. On the other hand, the nuclease from a related strain TCl-1, which has a less active enzyme of the same type, was successfully cloned.

Identification and characterization of nuclease activities in anaerobic environmental samples

DNA-degrading activity from anaerobic samples of bovine ruminal fluid, primary anaerobic digestor wastewater, freshwater sediments, and marine sediments was observed in the presence of 5 mM EDTA. Nuclease activity experiments involved exposing salmon chromosomal DNA to the environmental samples in 50 mM pH 7.2 buffer, incubating at 37°C, and subjecting the products to electrophoresis. The same stock and concentration of EDTA used in these assays (5 mM) completely inhibited commercial grade DNase. Nuclease activity in two of the samples, ruminal fluid and wastewater, was further characterized. DNA degradation in the ruminal sample was significantly reduced when EDTA or citrate concentrations were increased to 50 mM or above. DNA degradation activity in ruminal fluid was associated with material that passed through a 0.22-µm filter, but wastewater activity was associated with material retained by a 3-µm filter. Degradation activity in the wastewater was resistant to heat pretreatment, whereas the rumen activity was heat-labile (70°C, 60 min). These results demonstrated the biochemical complexity of these two environments and that high molecular weight DNA has a short half-life in these anaerobic environments.Key words: nucleic acid degradation, ruminal fluid, wastewater.

Do ruminal bacteria exchange genetic material?

This paper discusses the reasons and current evidence for gene transfer between ruminal bacteria and other bacteria in the environment, possible routes for genetic exchange, and candidate genes. Gene transfer between ruminal bacteria has been demonstrated in vitro; however, success has been only minimal in obtaining plasmids and other self-transmissible genetic material from ruminal bacteria. The application of molecular biology techniques with ruminal microorganisms should permit the opportunity for an in vivo assessment of gene transfer. Studies that could provide pertinent information for ruminal microbiologists and dairy nutritionists are outlined.

Isolation and characterization of Selenomonas ruminantium strains capable of 2-deoxyribose utilization

Microbes from ruminal contents of cattle were selectively enriched by using 2-deoxyribose (2DR) as a substrate for growth. Bacterial isolates growing on 2DR were gram-negative, curved, motile rods. The isolates grew on a broad range of substrates, including deoxyribose, glucose, ribose, mannitol, and lactate as well as ribonucleosides and deoxyribonucleosides. The strains also grew on rhamnose (6-deoxymannose) but not DNA. Organic acids produced from growth on hexoses and pentoses included acetate, propionate, lactate, and succinate. The isolates were identified as Selenomonas ruminantium subsp. lactilytica on the basis of morphology, substrate specificity, and other biochemical characteristics. Several characterized species of ruminal bacteria were also screened for growth on 2DR, with only one strain (S. ruminantium PC-18) found able to grow on 2DR. Ethanol was produced by 2DR when strains were grown on ribose or 2DR.

Extracellular deoxyribonucleases of streptococci: a comparison of their occurrence and levels of production among beta-hemolytic strains of various serological groups

Production of extracellular deoxyribonuclease by 394 strains of beta hemolytic streptococci was examined employing a deoxyribonucleic acid-methyl green assay. Enzymatic activities were measured in supernatants of bacterial cultures. Of the strains tested, 316 (80%) produced the enzyme. Nuclease production was demonstrated in 100% of group A strains and in 85, 74 and 58% of groups B, C and G, respectively. Levels of nuclease activity were then evaluated statistically. The analysis of variance showed that group A strains produced more enzyme than did streptococci of groups B, C or G. Group B strains produced less nuclease than did isolates of groups C or G. There was no significant difference in the levels of nuclease produced by groups C and G or by the various serological types of group B streptococci. Human group C strains produced more enzyme than animal strains.

Type II DNA restriction-modification system and an endonuclease from the ruminal bacterium Fibrobacter succinogenes S85

Fibrobacter succinogenes is an important cellulolytic bacterium found in the rumen and cecum of herbivores. Numerous attempts to introduce foreign DNA into F. succinogenes S85 have failed, suggesting the presence of genetic barriers in this organism. Results from this study clearly demonstrate that F. succinogenes S85 possesses a type II restriction endonuclease, FsuI, which recognizes the sequence 5'-GG(A/T)CC-3'. Analysis of the restriction products on sequencing gels showed that FsuI cleaves between the two deoxyguanosine residues, yielding a 3-base 5' protruding end. These data demonstrate that FsuI is an isoschizomer of AvaII. A methyltransferase activity has been identified in the cell extract of F. succinogenes S85. This activity modified DNA in vitro and protected the DNA from the restriction by FsuI and AvaII. DNA modified in vivo by a cloned methylase gene, which codes for M.Eco47II, also protected the DNA from restriction by FsuI, suggesting that FsuI is inhibited by methylation at one or both deoxycytosine residues of the recognition sequence. The methyltransferase activity in F. succinogenes S85 is likely modifying the same deoxycytosine residues, but the exact site(s) is unknown. A highly active DNase (DNase A) was also isolated from the cell extract of this organism. DNase A is an endonuclease which showed high activity on all forms of DNA (single stranded, double-stranded, linear, and circular) but no activity on RNA. In vitro, the DNase A hydrolyzed F. succinogenes S85 DNA extensively, indicating the lack of protection against hydrolysis by this enzyme. In the presence of Mg2+, DNA was hydrolyzed to fragments of 8 to 10 nucleotides in length. The presence of DNase A and the type II restriction-modification system of F. succinogenes S85 may be the barriers preventing the introduction of foreign DNA into this bacterium.