Lifu Song

Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey.

BackgroundCombating the action of plant pathogenic microorganisms by mycoparasitic fungi has been announced as an attractive biological alternative to the use of chemical fungicides since two decades. The fungal genus Trichoderma includes a high number of taxa which are able to recognize, combat and finally besiege and kill their prey. Only fragments of the biochemical processes related to this ability have been uncovered so far, however.ResultsWe analyzed genome-wide gene expression changes during the begin of physical contact between Trichoderma atroviride and two plant pathogens Botrytis cinerea and Rhizoctonia solani, and compared with gene expression patterns of mycelial and conidiating cultures, respectively. About 3000 ESTs, representing about 900 genes, were obtained from each of these three growth conditions. 66 genes, represented by 442 ESTs, were specifically and significantly overexpressed during onset of mycoparasitism, and the expression of a subset thereof was verified by expression analysis. The upregulated genes comprised 18 KOG groups, but were most abundant from the groups representing posttranslational processing, and amino acid metabolism, and included components of the stress response, reaction to nitrogen shortage, signal transduction and lipid catabolism. Metabolic network analysis confirmed the upregulation of the genes for amino acid biosynthesis and of those involved in the catabolism of lipids and aminosugars.ConclusionThe analysis of the genes overexpressed during the onset of mycoparasitism in T. atroviride has revealed that the fungus reacts to this condition with several previously undetected physiological reactions. These data enable a new and more comprehensive interpretation of the physiology of mycoparasitism, and will aid in the selection of traits for improvement of biocontrol strains by recombinant techniques.

Novel (2R,3R)-2,3-Butanediol Dehydrogenase from Potential Industrial Strain Paenibacillus polymyxa ATCC 12321

ABSTRACT A (2R,3R)-2,3-butanediol dehydrogenase (BDH99::67) from Paenibacillus polymyxa ATCC 12321 was functionally characterized. The genetic characteristics of BDH99::67 are completely different from those of meso- and (2S,3S)-2,3-butanediol dehydrogenases. The results showed that BDH99::67 belongs to the medium-chain dehydrogenase/reductase superfamily and not to the short-chain dehydrogenase/reductase superfamily, to which meso- and (2S,3S)-2,3-butanediol dehydrogenases belong.

A genome-wide study of two-component signal transduction systems in eight newly sequenced mutans streptococci strains

BackgroundMutans streptococci are a group of gram-positive bacteria including the primary cariogenic dental pathogen Streptococcus mutans and closely related species. Two component systems (TCSs) composed of a signal sensing histidine kinase (HK) and a response regulator (RR) play key roles in pathogenicity, but have not been comparatively studied for these oral bacterial pathogens.ResultsHKs and RRs of 8 newly sequenced mutans streptococci strains, including S. sobrinus DSM20742, S. ratti DSM20564 and six S. mutans strains, were identified and compared to the TCSs of S. mutans UA159 and NN2025, two previously genome sequenced S. mutans strains. Ortholog analysis revealed 18 TCS clusters (HK-RR pairs), 2 orphan HKs and 2 orphan RRs, of which 8 TCS clusters were common to all 10 strains, 6 were absent in one or more strains, and the other 4 were exclusive to individual strains. Further classification of the predicted HKs and RRs revealed interesting aspects of their putative functions. While TCS complements were comparable within the six S. mutans strains, S. sobrinus DSM20742 lacked TCSs possibly involved in acid tolerance and fructan catabolism, and S. ratti DSM20564 possessed 3 unique TCSs but lacked the quorum-sensing related TCS (ComDE). Selected computational predictions were verified by PCR experiments.ConclusionsDifferences in the TCS repertoires of mutans streptococci strains, especially those of S. sobrinus and S. ratti in comparison to S. mutans, imply differences in their response mechanisms for survival in the dynamic oral environment. This genomic level study of TCSs should help in understanding the pathogenicity of these mutans streptococci strains.

Draft Genome Sequence of Type Strain Clostridium pasteurianum DSM 525 (ATCC 6013), a Promising Producer of Chemicals and Fuels

ABSTRACT Clostridium pasteurianum, an anaerobic bacterium able to utilize atmospheric free nitrogen for biosynthesis, has recently been proven to be a promising producer of chemicals and fuels, such as 1,3-propanediol and n-butanol. Here, we report the high-quality draft genome sequence of DSM 525, a type strain of C. pasteurianum.

Comparing the cariogenic species Streptococcus sobrinus and S. mutans on whole genome level

Background Two closely related species of mutans streptococci, namely Streptococcus mutans and Streptococcus sobrinus, are associated with dental caries in humans. Their acidogenic and aciduric capacity is directly associated with the cariogenic potential of these bacteria. To survive acidic and temporarily harsh conditions in the human oral cavity with hundreds of other microbial co-colonizers as competitors, both species have developed numerous mechanisms for adaptation. Objectives The recently published novel genome information for both species is used to elucidate genetic similarities but especially differences and to discuss the impact on cariogenicity of the corresponding phenotypic properties including adhesion, carbohydrate uptake and fermentation, acid tolerance, signaling by two component systems, competence, and oxidative stress resistance. Conclusions S. sobrinus can down-regulate the SpaA-mediated adherence to the pellicle. It has a smaller number of two-component signaling systems and bacteriocin-related genes than S. mutans, but all or even more immunity proteins. It lacks the central competence genes comC, comS, and comR. There are more genes coding for glucosyltransferases and a novel energy production pathway formed by lactate oxidase, which is not found in S. mutans. Both species show considerable differences in the regulation of fructan catabolism. However, both S. mutans and S. sobrinus share most of these traits and should therefore be considered as equally virulent with regard to dental caries.

Genetic variability of mutans streptococci revealed by wide whole-genome sequencing

BackgroundMutans streptococci are a group of bacteria significantly contributing to tooth decay. Their genetic variability is however still not well understood.ResultsGenomes of 6 clinical S. mutans isolates of different origins, one isolate of S. sobrinus (DSM 20742) and one isolate of S. ratti (DSM 20564) were sequenced and comparatively analyzed. Genome alignment revealed a mosaic-like structure of genome arrangement. Genes related to pathogenicity are found to have high variations among the strains, whereas genes for oxidative stress resistance are well conserved, indicating the importance of this trait in the dental biofilm community. Analysis of genome-scale metabolic networks revealed significant differences in 42 pathways. A striking dissimilarity is the unique presence of two lactate oxidases in S. sobrinus DSM 20742, probably indicating an unusual capability of this strain in producing H2O2 and expanding its ecological niche. In addition, lactate oxidases may form with other enzymes a novel energetic pathway in S. sobrinus DSM 20742 that can remedy its deficiency in citrate utilization pathway.Using 67 S. mutans genomes currently available including the strains sequenced in this study, we estimates the theoretical core genome size of S. mutans, and performed modeling of S. mutans pan-genome by applying different fitting models. An “open” pan-genome was inferred.ConclusionsThe comparative genome analyses revealed diversities in the mutans streptococci group, especially with respect to the virulence related genes and metabolic pathways. The results are helpful for better understanding the evolution and adaptive mechanisms of these oral pathogen microorganisms and for combating them.

Genome sequence of type strain Paenibacillus polymyxa DSM 365, a highly efficient producer of optically active (R,R)-2,3-butanediol

Paenibacillus polymyxa DSM 365, an efficient producer of (R,R)-2,3-butanediol, is known to show the highest production titer and productivity reported to date. Here, the first draft genome sequence of this promising strain may provide the genetic basis for further insights into the molecular mechanisms underlying the production of (R,R)-2,3-butanediol with high optical purity and at a high titer. It will also facilitate the design of rational strategies for further strain improvements, as well as construction of artificial biosynthetic pathways through synthetic biology for asymmetric synthesis of chiral 2,3-butanediol or acetoin in common microbial hosts.

Genome Sequence of Bacillus coagulans P38, an Efficient Polymer-Grade l-Lactate Producer from Cellulosic Substrates

ABSTRACT Bacillus coagulans P38 is an efficient polymer-grade l-lactic acid producer from a cellulosic carbon source. Here, the draft 3.37-Mb genome sequence of this potential strain may provide useful information to further improve the strain performance for higher titers and, importantly, to understand the mechanism of its high tolerance for 2-furfural.

Orthogonal Information Encoding in Living Cells with High Error-Tolerance, Safety, and Fidelity

Information encoding in DNA is of great interest but its applications in vivo might be questionable since errors could be enriched exponentially by cellular replications and the artificial sequences may interfere with the natural ones. Here, a novel self-error-detecting, three-base block encoding scheme (SED3B) is proposed for reliable and orthogonal information encoding in living cells. SED3B utilizes a novel way to add error detecting bases in small data blocks which can combine with the inherent redundancy of DNA molecules for effective error correction. Errors at a rate of 19% can be corrected as shown by error-prone PCR experiments with E. coli cells. Calculations based on this preliminary result show that SED3B encoded information in E. coli can be reliable for more than 12 000 years of continuous replication. Importantly, SED3B encoded sequences do not share sequence space to all reported natural DNA sequences except for some short tandem repeats, indicating a low biological relevance of encoded sequences for the first time. These features make SED3B attractive for broad orthogonal information encoding purposes in living cells, for example, comments/barcodes encoding in synthetic biology. For proof of concept, 10 different barcodes were encoded in E. coli cells. After continuous replications for 10 days including exposure to ultraviolet for 2-3 min (lethality >60%) per day, all barcodes were fully recovered, proving the stability of the encoded information. An online encoding-decoding system is implemented and available at http://biosystem.bt1.tu-harburg.de/sed3b/ .

Genome Sequence of Tumebacillus flagellatus GST4, the First Genome Sequence of a Species in the Genus Tumebacillus.

ABSTRACT We present here the first genome sequence of a species in the genus Tumebacillus. The draft genome sequence of Tumebacillus flagellatus GST4 provides a genetic basis for future studies addressing the origins, evolution, and ecological role of Tumebacillus organisms, as well as a source of acid-resistant amylase-encoding genes for further studies.