Dandekar T

References (5)

Title : Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges - Siegl_2011_ISME.J_5_61
Author(s) : Siegl A , Kamke J , Hochmuth T , Piel J , Richter M , Liang C , Dandekar T , Hentschel U
Ref : Isme J , 5 :61 , 2011
Abstract : In this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum Poribacteria, members of which are nearly exclusively found in marine sponges. The microbial consortia of the Mediterranean sponge Aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial cells were subjected to phi29 polymerase-mediated 'whole-genome amplification'. Pyrosequencing of a single amplified genome (SAG) derived from a member of the Poribacteria resulted in nearly 1.6 Mb of genomic information distributed among 554 contigs analyzed in this study. Approximately two-third of the poribacterial genome was sequenced. Our findings shed light on the functional properties and lifestyle of a possibly ancient bacterial symbiont of marine sponges. The Poribacteria are mixotrophic bacteria with autotrophic CO(2)-fixation capacities through the Wood-Ljungdahl pathway. The cell wall is of Gram-negative origin. The Poribacteria produce at least two polyketide synthases (PKSs), one of which is the sponge-specific Sup-type PKS. Several putative symbiosis factors such as adhesins (bacterial Ig-like domains, lamininin G domain proteins), adhesin-related proteins (ankyrin, fibronectin type III) and tetratrico peptide repeat domain-encoding proteins were identified, which might be involved in mediating sponge-microbe interactions. The discovery of genes coding for 24-isopropyl steroids implies that certain fossil biomarkers used to date the origins of metazoan life on earth may possibly be of poribacterial origin. Single-cell genomic approaches, such as those shown herein, contribute to a better understanding of beneficial microbial consortia, of which most members are, because of the lack of cultivation, inaccessible by conventional techniques.
ESTHER : Siegl_2011_ISME.J_5_61
PubMedSearch : Siegl_2011_ISME.J_5_61
PubMedID: 20613790

Title : The highly attenuated oncolytic recombinant vaccinia virus GLV-1h68: comparative genomic features and the contribution of F14.5L inactivation - Zhang_2009_Mol.Genet.Genomics_282_417
Author(s) : Zhang Q , Liang C , Yu YA , Chen N , Dandekar T , Szalay AA
Ref : Mol Genet Genomics , 282 :417 , 2009
Abstract : As a new anticancer treatment option, vaccinia virus (VACV) has shown remarkable antitumor activities (oncolysis) in preclinical studies, but potential infection of other organs remains a safety concern. We present here genome comparisons between the de novo sequence of GLV-1h68, a recombinant VACV, and other VACVs. The identified differences in open reading frames (ORFs) include genes encoding host-range selection, virulence and immune modulation proteins, e.g., ankyrin-like proteins, serine proteinase inhibitor SPI-2/CrmA, tumor necrosis factor (TNF) receptor homolog CrmC, semaphorin-like and interleukin-1 receptor homolog proteins. Phylogenetic analyses indicate that GLV-1h68 is closest to Lister strains but has lost several ORFs present in its parental LIVP strain, including genes encoding CrmE and a viral Golgi anti-apoptotic protein, v-GAAP. The reduced pathogenicity of GLV-1h68 is confirmed in male mice bearing C6 rat glioma and in immunocompetent mice bearing B16-F10 murine melanoma. The contribution of foreign gene expression cassettes in the F14.5L, J2R and A56R loci is analyzed, in particular the contribution of F14.5L inactivation to the reduced virulence is demonstrated by comparing the virulence of GLV-1h68 with its F14.5L-null and revertant viruses. GLV-1h68 is a promising engineered VACV variant for anticancer therapy with tumor-specific replication, reduced pathogenicity and benign tissue tropism.
ESTHER : Zhang_2009_Mol.Genet.Genomics_282_417
PubMedSearch : Zhang_2009_Mol.Genet.Genomics_282_417
PubMedID: 19701652
Gene_locus related to this paper: cowvi-M5L

Title : The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali' - Kube_2008_BMC.Genomics_9_306
Author(s) : Kube M , Schneider B , Kuhl H , Dandekar T , Heitmann K , Migdoll AM , Reinhardt R , Seemuller E
Ref : BMC Genomics , 9 :306 , 2008
Abstract : BACKGROUND: Phytoplasmas are insect-transmitted, uncultivable bacterial plant pathogens that cause diseases in hundreds of economically important plants. They represent a monophyletic group within the class Mollicutes (trivial name mycoplasmas) and are characterized by a small genome with a low GC content, and the lack of a firm cell wall. All mycoplasmas, including strains of 'Candidatus (Ca.) Phytoplasma asteris' and 'Ca. P. australiense', examined so far have circular chromosomes, as is the case for almost all walled bacteria. RESULTS: Our work has shown that 'Ca. Phytoplasma mali', the causative agent of apple proliferation disease, has a linear chromosome. Linear chromosomes were also identified in the closely related provisional species 'Ca. P. pyri' and 'Ca. P. prunorum'. The chromosome of 'Ca. P. mali' strain AT is 601,943 bp in size and has a GC content of 21.4%. The chromosome is further characterized by large terminal inverted repeats and covalently closed hairpin ends. Analysis of the protein-coding genes revealed that glycolysis, the major energy-yielding pathway supposed for 'Ca. P. asteris', is incomplete in 'Ca. P. mali'. Due to the apparent lack of other metabolic pathways present in mycoplasmas, it is proposed that maltose and malate are utilized as carbon and energy sources. However, complete ATP-yielding pathways were not identified. 'Ca. P. mali' also differs from 'Ca. P. asteris' by a smaller genome, a lower GC content, a lower number of paralogous genes, fewer insertions of potential mobile DNA elements, and a strongly reduced number of ABC transporters for amino acids. In contrast, 'Ca. P. mali' has an extended set of genes for homologous recombination, excision repair and SOS response than 'Ca. P. asteris'. CONCLUSION: The small linear chromosome with large terminal inverted repeats and covalently closed hairpin ends, the extremely low GC content and the limited metabolic capabilities reflect unique features of 'Ca. P. mali', not only within phytoplasmas, but all mycoplasmas. It is expected that the genome information obtained here will contribute to a better understanding of the reduced metabolism of phytoplasmas, their fastidious nutrition requirements that prevented axenic cultivation, and the mechanisms involved in pathogenicity.
ESTHER : Kube_2008_BMC.Genomics_9_306
PubMedSearch : Kube_2008_BMC.Genomics_9_306
PubMedID: 18582369
Gene_locus related to this paper: phymt-b3qzy9

Title : Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes - Hain_2006_J.Bacteriol_188_7405
Author(s) : Hain T , Steinweg C , Kuenne CT , Billion A , Ghai R , Chatterjee SS , Domann E , Karst U , Goesmann A , Bekel T , Bartels D , Kaiser O , Meyer F , Puhler A , Weisshaar B , Wehland J , Liang C , Dandekar T , Lampidis R , Kreft J , Goebel W , Chakraborty T
Ref : Journal of Bacteriology , 188 :7405 , 2006
Abstract : We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the genus Listeria. Listeria welshimeri harbors a circular chromosome of 2,814,130 bp with 2,780 open reading frames. Comparative genomic analysis of chromosomal regions between L. welshimeri, Listeria innocua, and Listeria monocytogenes shows strong overall conservation of synteny, with the exception of the translocation of an F(o)F(1) ATP synthase. The smaller size of the L. welshimeri genome is the result of deletions in all of the genes involved in virulence and of "fitness" genes required for intracellular survival, transcription factors, and LPXTG- and LRR-containing proteins as well as 55 genes involved in carbohydrate transport and metabolism. In total, 482 genes are absent from L. welshimeri relative to L. monocytogenes. Of these, 249 deletions are commonly absent in both L. welshimeri and L. innocua, suggesting similar genome evolutionary paths from an ancestor. We also identified 311 genes specific to L. welshimeri that are absent in the other two species, indicating gene expansion in L. welshimeri, including horizontal gene transfer. The species L. welshimeri appears to have been derived from early evolutionary events and an ancestor more compact than L. monocytogenes that led to the emergence of nonpathogenic Listeria spp.
ESTHER : Hain_2006_J.Bacteriol_188_7405
PubMedSearch : Hain_2006_J.Bacteriol_188_7405
PubMedID: 16936040
Gene_locus related to this paper: lisin-LIN0976 , lisin-LIN2544 , lismo-LMO2089 , lismo-LMO2452 , lismo-LMO2453 , lismo-metx , lisss-d3urb3 , lisw6-a0agy6 , lisw6-a0ajc8 , lisw6-a0am12

Title : Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames - Dandekar_2000_Nucleic.Acids.Res_28_3278
Author(s) : Dandekar T , Huynen M , Regula JT , Ueberle B , Zimmermann CU , Andrade MA , Doerks T , Sanchez-Pulido L , Snel B , Suyama M , Yuan YP , Herrmann R , Bork P
Ref : Nucleic Acids Research , 28 :3278 , 2000
Abstract : Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10 new proteins were predicted in intergenic regions, two further were newly identified by mass spectrometry and one protein ORF was dismissed) and the number of RNAs from 39 to 42 genes. For 19 of the now 35 tRNAs and for six other functional RNAs the exact genome positions were re-annotated and two new tRNA(Leu) and a small 200 nt RNA were identified. Sixteen protein reading frames were extended and eight shortened. For each ORF a consistent annotation vocabulary has been introduced. Annotation reasoning, annotation categories and comparisons to other published data on M.pneumoniae functional assignments are given. Experimental evidence includes 2-dimensional gel electrophoresis in combination with mass spectrometry as well as gene expression data from this study. Compared to the original annotation, we increased the number of proteins with predicted functional features from 349 to 458. The increase includes 36 new predictions and 73 protein assignments confirmed by the published literature. Furthermore, there are 23 reductions and 30 additions with respect to the previous annotation. mRNA expression data support transcription of 184 of the functionally unassigned reading frames.
ESTHER : Dandekar_2000_Nucleic.Acids.Res_28_3278
PubMedSearch : Dandekar_2000_Nucleic.Acids.Res_28_3278
PubMedID: 10954595
Gene_locus related to this paper: mycpn-pip