2014
Bauer, Eugen; Salem, Hassan; Marz, Manja; Vogel, Heiko; Kaltenpoth, Martin
In: PLoS One, vol. 9, pp. e114865, 2014.
Abstract | Links | BibTeX | Tags: annotation, assembly, bacteria, differential expression analysis, insects, RNA / transcriptomics
@article{Bauer:14,
title = {Transcriptomic immune response of the cotton stainer \textit{Dysdercus fasciatus} to experimental elimination of vitamin-supplementing intestinal symbionts},
author = {Eugen Bauer and Hassan Salem and Manja Marz and Heiko Vogel and Martin Kaltenpoth},
url = {http://www.ebi.ac.uk/ena/data/view/PRJEB6171},
doi = {10.1371/journal.pone.0114865},
year = {2014},
date = {2014-12-09},
urldate = {2014-12-09},
journal = {PLoS One},
volume = {9},
pages = {e114865},
abstract = {The acquisition and vertical transmission of bacterial symbionts plays an important role in insect evolution and ecology. However, the molecular mechanisms underlying the stable maintenance and control of mutualistic bacteria remain poorly understood. The cotton stainer Dysdercus fasciatus harbours the actinobacterial symbionts Coriobacterium glomerans and Gordonibacter sp. in its midgut. The symbionts supplement limiting B vitamins and thereby significantly contribute to the host's fitness. In this study, we experimentally disrupted the symbionts' vertical transmission route and performed comparative transcriptomic analyses of genes expressed in the gut of aposymbiotic (symbiont-free) and control individuals to study the host immune response in presence and absence of the mutualists. Annotation of assembled cDNA reads identified a considerable number of genes involved in the innate immune system, including different protein isoforms of several immune effector proteins (specifically i-type lysozyme, defensin, hemiptericin, and pyrrhocoricin), suggesting the possibility for a highly differentiated response towards the complex resident microbial community. Gene expression analyses revealed a constitutive expression of transcripts involved in signal transduction of the main insect immune pathways, but differential expression of certain antimicrobial peptide genes. Specifically, qPCRs confirmed the significant down-regulation of c-type lysozyme and up-regulation of hemiptericin in aposymbiotic individuals. The high expression of c-type lysozyme in symbiont-containing bugs may serve to lyse symbiont cells and thereby harvest B-vitamins that are necessary for subsistence on the deficient diet of Malvales seeds. Our findings suggest a sophisticated host response to perturbation of the symbiotic gut microbiota, indicating that the innate immune system not only plays an important role in combating pathogens, but also serves as a communication interface between host and symbionts.},
keywords = {annotation, assembly, bacteria, differential expression analysis, insects, RNA / transcriptomics},
pubstate = {published},
tppubtype = {article}
}
The acquisition and vertical transmission of bacterial symbionts plays an important role in insect evolution and ecology. However, the molecular mechanisms underlying the stable maintenance and control of mutualistic bacteria remain poorly understood. The cotton stainer Dysdercus fasciatus harbours the actinobacterial symbionts Coriobacterium glomerans and Gordonibacter sp. in its midgut. The symbionts supplement limiting B vitamins and thereby significantly contribute to the host's fitness. In this study, we experimentally disrupted the symbionts' vertical transmission route and performed comparative transcriptomic analyses of genes expressed in the gut of aposymbiotic (symbiont-free) and control individuals to study the host immune response in presence and absence of the mutualists. Annotation of assembled cDNA reads identified a considerable number of genes involved in the innate immune system, including different protein isoforms of several immune effector proteins (specifically i-type lysozyme, defensin, hemiptericin, and pyrrhocoricin), suggesting the possibility for a highly differentiated response towards the complex resident microbial community. Gene expression analyses revealed a constitutive expression of transcripts involved in signal transduction of the main insect immune pathways, but differential expression of certain antimicrobial peptide genes. Specifically, qPCRs confirmed the significant down-regulation of c-type lysozyme and up-regulation of hemiptericin in aposymbiotic individuals. The high expression of c-type lysozyme in symbiont-containing bugs may serve to lyse symbiont cells and thereby harvest B-vitamins that are necessary for subsistence on the deficient diet of Malvales seeds. Our findings suggest a sophisticated host response to perturbation of the symbiotic gut microbiota, indicating that the innate immune system not only plays an important role in combating pathogens, but also serves as a communication interface between host and symbionts.
Salem, Hassan; Bauer, Eugen; Strauss, Anja S; Vogel, Heiko; Marz, Manja; Kaltenpoth, Martin
Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host Journal Article
In: Proc Biol Sci, vol. 281, pp. 20141838, 2014.
Abstract | Links | BibTeX | Tags: bacteria, differential expression analysis, insects, RNA / transcriptomics
@article{Salem:14,
title = {Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host},
author = {Hassan Salem and Eugen Bauer and Anja S Strauss and Heiko Vogel and Manja Marz and Martin Kaltenpoth},
doi = {10.1098/rspb.2014.1838},
year = {2014},
date = {2014-12-07},
urldate = {2014-12-07},
journal = {Proc Biol Sci},
volume = {281},
pages = {20141838},
abstract = {Despite the demonstrated functional importance of gut microbes, our understanding of how animals regulate their metabolism in response to nutritionally beneficial symbionts remains limited. Here, we elucidate the functional importance of the African cotton stainer's (Dysdercus fasciatus) association with two actinobacterial gut symbionts and subsequently examine the insect's transcriptional response following symbiont elimination. In line with bioassays demonstrating the symbionts' contribution towards host fitness through the supplementation of B vitamins, comparative transcriptomic analyses of genes involved in import and processing of B vitamins revealed an upregulation of gene expression in aposymbiotic (symbiont-free) compared with symbiotic individuals; an expression pattern that is indicative of B vitamin deficiency in animals. Normal expression levels of these genes, however, can be restored by either artificial supplementation of B vitamins into the insect's diet or reinfection with the actinobacterial symbionts. Furthermore, the functional characterization of the differentially expressed thiamine transporter 2 through heterologous expression in Xenopus laevis oocytes confirms its role in cellular uptake of vitamin B1. These findings demonstrate that despite an extracellular localization, beneficial gut microbes can be integral to the host's metabolic homeostasis, reminiscent of bacteriome-localized intracellular mutualists.},
keywords = {bacteria, differential expression analysis, insects, RNA / transcriptomics},
pubstate = {published},
tppubtype = {article}
}
Despite the demonstrated functional importance of gut microbes, our understanding of how animals regulate their metabolism in response to nutritionally beneficial symbionts remains limited. Here, we elucidate the functional importance of the African cotton stainer's (Dysdercus fasciatus) association with two actinobacterial gut symbionts and subsequently examine the insect's transcriptional response following symbiont elimination. In line with bioassays demonstrating the symbionts' contribution towards host fitness through the supplementation of B vitamins, comparative transcriptomic analyses of genes involved in import and processing of B vitamins revealed an upregulation of gene expression in aposymbiotic (symbiont-free) compared with symbiotic individuals; an expression pattern that is indicative of B vitamin deficiency in animals. Normal expression levels of these genes, however, can be restored by either artificial supplementation of B vitamins into the insect's diet or reinfection with the actinobacterial symbionts. Furthermore, the functional characterization of the differentially expressed thiamine transporter 2 through heterologous expression in Xenopus laevis oocytes confirms its role in cellular uptake of vitamin B1. These findings demonstrate that despite an extracellular localization, beneficial gut microbes can be integral to the host's metabolic homeostasis, reminiscent of bacteriome-localized intracellular mutualists.
2012
Lechner, Marcus; Marz, Manja; Ihling, Christian; Sinz, Andrea; Stadler, Peter F; Krauss, Veiko
The correlation of genome size and DNA methylation rate in metazoans Journal Article
In: Theory Biosci, vol. 132, pp. 47–60, 2012.
Abstract | Links | BibTeX | Tags: DNA / genomics, evolution, insects, nucleic acid modifications, phylogenetics
@article{Lechner:13,
title = {The correlation of genome size and DNA methylation rate in metazoans},
author = {Marcus Lechner and Manja Marz and Christian Ihling and Andrea Sinz and Peter F Stadler and Veiko Krauss},
doi = {10.1007/s12064-012-0167-y},
year = {2012},
date = {2012-11-07},
urldate = {2012-11-07},
journal = {Theory Biosci},
volume = {132},
pages = {47--60},
abstract = {Total DNA methylation rates are well known to vary widely between different metazoans. The phylogenetic distribution of this variation, however, has not been investigated systematically. We combine here publicly available data on methylcytosine content with the analysis of nucleotide compositions of genomes and transcriptomes of 78 metazoan species to trace the evolution of abundance and distribution of DNA methylation. The depletion of CpG and the associated enrichment of TpG and CpA dinucleotides are used to infer the intensity and localization of germline CpG methylation and to estimate its evolutionary dynamics. We observe a positive correlation of the relative methylation of CpG motifs with genome size. We tested this trend successfully by measuring total DNA methylation with LC/MS in orthopteran insects with very different genome sizes: house crickets, migratory locusts and meadow grasshoppers. We hypothesize that the observed correlation between methylation rate and genome size is due to a dependence of both variables from long-term effective population size and is driven by the accumulation of repetitive sequences that are typically methylated during periods of small population sizes. This process may result in generally methylated, large genomes such as those of jawed vertebrates. In this case, the emergence of a novel demethylation pathway and of novel reader proteins for methylcytosine may have enabled the usage of cytosine methylation for promoter-based gene regulation. On the other hand, persistently large populations may lead to a compression of the genome and to the loss of the DNA methylation machinery, as observed, e.g., in nematodes.},
keywords = {DNA / genomics, evolution, insects, nucleic acid modifications, phylogenetics},
pubstate = {published},
tppubtype = {article}
}
Total DNA methylation rates are well known to vary widely between different metazoans. The phylogenetic distribution of this variation, however, has not been investigated systematically. We combine here publicly available data on methylcytosine content with the analysis of nucleotide compositions of genomes and transcriptomes of 78 metazoan species to trace the evolution of abundance and distribution of DNA methylation. The depletion of CpG and the associated enrichment of TpG and CpA dinucleotides are used to infer the intensity and localization of germline CpG methylation and to estimate its evolutionary dynamics. We observe a positive correlation of the relative methylation of CpG motifs with genome size. We tested this trend successfully by measuring total DNA methylation with LC/MS in orthopteran insects with very different genome sizes: house crickets, migratory locusts and meadow grasshoppers. We hypothesize that the observed correlation between methylation rate and genome size is due to a dependence of both variables from long-term effective population size and is driven by the accumulation of repetitive sequences that are typically methylated during periods of small population sizes. This process may result in generally methylated, large genomes such as those of jawed vertebrates. In this case, the emergence of a novel demethylation pathway and of novel reader proteins for methylcytosine may have enabled the usage of cytosine methylation for promoter-based gene regulation. On the other hand, persistently large populations may lead to a compression of the genome and to the loss of the DNA methylation machinery, as observed, e.g., in nematodes.
2011
Dilcher, Meik; Hasib, Lekbira; Lechner, Marcus; Wieseke, Nicolas; Middendorf, Martin; Marz, Manja; Koch, Andrea; Spiegel, Martin; Dobler, Gerhard; Hufert, Frank T; Weidmann, Manfred
Genetic characterization of Tribeč virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses Journal Article
In: Virology, vol. 423, pp. 68–76, 2011.
Abstract | Links | BibTeX | Tags: classification, evolution, insects, phylogenetics, virus host interaction, viruses
@article{Dilcher:12,
title = {Genetic characterization of Tribeč virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses},
author = {Meik Dilcher and Lekbira Hasib and Marcus Lechner and Nicolas Wieseke and Martin Middendorf and Manja Marz and Andrea Koch and Martin Spiegel and Gerhard Dobler and Frank T Hufert and Manfred Weidmann},
doi = {10.1016/j.virol.2011.11.020},
year = {2011},
date = {2011-12-20},
urldate = {2011-12-20},
journal = {Virology},
volume = {423},
pages = {68--76},
abstract = {We determined the complete genome sequences of Tribeč virus (TRBV) and Kemerovo virus (KEMV), two tick-transmitted Orbiviruses that can cause diseases of the central nervous system and that are currently classified into the Great Island virus serogroup. VP2 proteins of TRBV and KEMV show very low sequence similarity to the homologous VP4 protein of tick-transmitted Great Island virus (GIV). The new sequence data support previous serological classification of these Orbiviruses into the Kemerovo serogroup, which is different from the Great Island virus serogroup. Genome segment 9 of TRBV and KEMV encodes several overlapping ORF's in the +1 reading frame relative to VP6(Hel). A co-phylogenetic analysis indicates a host switch from insect-borne Orbiviruses toward Ixodes species, which is in disagreement with previously published data.},
keywords = {classification, evolution, insects, phylogenetics, virus host interaction, viruses},
pubstate = {published},
tppubtype = {article}
}
We determined the complete genome sequences of Tribeč virus (TRBV) and Kemerovo virus (KEMV), two tick-transmitted Orbiviruses that can cause diseases of the central nervous system and that are currently classified into the Great Island virus serogroup. VP2 proteins of TRBV and KEMV show very low sequence similarity to the homologous VP4 protein of tick-transmitted Great Island virus (GIV). The new sequence data support previous serological classification of these Orbiviruses into the Kemerovo serogroup, which is different from the Great Island virus serogroup. Genome segment 9 of TRBV and KEMV encodes several overlapping ORF's in the +1 reading frame relative to VP6(Hel). A co-phylogenetic analysis indicates a host switch from insect-borne Orbiviruses toward Ixodes species, which is in disagreement with previously published data.
2009
Hiller, Michael; Findeiss, Sven; Lein, Sandro; Marz, Manja; Nickel, Claudia; Rose, Dominic; Schulz, Christine; Backofen, Rolf; Prohaska, Sonja J; Reuter, Gunter; Stadler, Peter F
Conserved introns reveal novel transcripts in Drosophila melanogaster Journal Article
In: Genome Res, vol. 19, pp. 1289–1300, 2009.
Abstract | Links | BibTeX | Tags: insects, ncRNAs, RNA structure
@article{Hiller:09,
title = {Conserved introns reveal novel transcripts in \textit{Drosophila melanogaster}},
author = {Michael Hiller and Sven Findeiss and Sandro Lein and Manja Marz and Claudia Nickel and Dominic Rose and Christine Schulz and Rolf Backofen and Sonja J Prohaska and Gunter Reuter and Peter F Stadler},
doi = {10.1101/gr.090050.108},
year = {2009},
date = {2009-05-20},
urldate = {2009-05-20},
journal = {Genome Res},
volume = {19},
pages = {1289--1300},
abstract = {Noncoding RNAs that are-like mRNAs-spliced, capped, and polyadenylated have important functions in cellular processes. The inventory of these mRNA-like noncoding RNAs (mlncRNAs), however, is incomplete even in well-studied organisms, and so far, no computational methods exist to predict such RNAs from genomic sequences only. The subclass of these transcripts that is evolutionarily conserved usually has conserved intron positions. We demonstrate here that a genome-wide comparative genomics approach searching for short conserved introns is capable of identifying conserved transcripts with a high specificity. Our approach requires neither an open reading frame nor substantial sequence or secondary structure conservation in the surrounding exons. Thus it identifies spliced transcripts in an unbiased way. After applying our approach to insect genomes, we predict 369 introns outside annotated coding transcripts, of which 131 are confirmed by expressed sequence tags (ESTs) and/or noncoding FlyBase transcripts. Of the remaining 238 novel introns, about half are associated with protein-coding genes-either extending coding or untranslated regions or likely belonging to unannotated coding genes. The remaining 129 introns belong to novel mlncRNAs that are largely unstructured. Using RT-PCR, we verified seven of 12 tested introns in novel mlncRNAs and 11 of 17 introns in novel coding genes. The expression level of all verified mlncRNA transcripts is low but varies during development, which suggests regulation. As conserved introns indicate both purifying selection on the exon-intron structure and conserved expression of the transcript in related species, the novel mlncRNAs are good candidates for functional transcripts.},
keywords = {insects, ncRNAs, RNA structure},
pubstate = {published},
tppubtype = {article}
}
Noncoding RNAs that are-like mRNAs-spliced, capped, and polyadenylated have important functions in cellular processes. The inventory of these mRNA-like noncoding RNAs (mlncRNAs), however, is incomplete even in well-studied organisms, and so far, no computational methods exist to predict such RNAs from genomic sequences only. The subclass of these transcripts that is evolutionarily conserved usually has conserved intron positions. We demonstrate here that a genome-wide comparative genomics approach searching for short conserved introns is capable of identifying conserved transcripts with a high specificity. Our approach requires neither an open reading frame nor substantial sequence or secondary structure conservation in the surrounding exons. Thus it identifies spliced transcripts in an unbiased way. After applying our approach to insect genomes, we predict 369 introns outside annotated coding transcripts, of which 131 are confirmed by expressed sequence tags (ESTs) and/or noncoding FlyBase transcripts. Of the remaining 238 novel introns, about half are associated with protein-coding genes-either extending coding or untranslated regions or likely belonging to unannotated coding genes. The remaining 129 introns belong to novel mlncRNAs that are largely unstructured. Using RT-PCR, we verified seven of 12 tested introns in novel mlncRNAs and 11 of 17 introns in novel coding genes. The expression level of all verified mlncRNA transcripts is low but varies during development, which suggests regulation. As conserved introns indicate both purifying selection on the exon-intron structure and conserved expression of the transcript in related species, the novel mlncRNAs are good candidates for functional transcripts.
2008
Marz, Manja; Kirsten, Toralf; Stadler, Peter F
Evolution of spliceosomal snRNA genes in metazoan animals Journal Article
In: J Mol Evol, vol. 67, pp. 594–607, 2008.
Abstract | Links | BibTeX | Tags: evolution, insects, ncRNAs, RNA structure, splicing
@article{Marz:08,
title = {Evolution of spliceosomal snRNA genes in metazoan animals},
author = {Manja Marz and Toralf Kirsten and Peter F Stadler},
doi = {10.1007/s00239-008-9149-6},
year = {2008},
date = {2008-11-22},
urldate = {2008-11-22},
journal = {J Mol Evol},
volume = {67},
pages = {594--607},
abstract = {While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs were detected in nematodes or in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralogue groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit, in particular, U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.},
keywords = {evolution, insects, ncRNAs, RNA structure, splicing},
pubstate = {published},
tppubtype = {article}
}
While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs were detected in nematodes or in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralogue groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit, in particular, U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.
Marz, Manja; Mosig, Axel; Stadler, Bärbel M R; Stadler, Peter F
U7 snRNAs: a computational survey Journal Article
In: Genomics Proteomics Bioinformatics, vol. 5, no. 3-4, pp. 187–195, 2008.
Abstract | Links | BibTeX | Tags: evolution, insects, ncRNAs, RNA structure
@article{Marz:07,
title = {U7 snRNAs: a computational survey},
author = {Manja Marz and Axel Mosig and Bärbel M R Stadler and Peter F Stadler},
doi = {10.1016/S1672-0229(08)60006-6},
year = {2008},
date = {2008-02-08},
urldate = {2008-02-08},
journal = {Genomics Proteomics Bioinformatics},
volume = {5},
number = {3-4},
pages = {187--195},
abstract = {U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for functional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase II. Based on the results of this search, we discuss the high variability of U7 snRNAs in both sequence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short sequence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.},
keywords = {evolution, insects, ncRNAs, RNA structure},
pubstate = {published},
tppubtype = {article}
}
U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for functional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase II. Based on the results of this search, we discuss the high variability of U7 snRNAs in both sequence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short sequence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.