Li, C.C.Y. et al. (2017) International Worm Meeting "Towards a unified global C. elegans Metabolic Reconstruction Model."

Li, C.C.Y., Witting, M., Kaleta, C., Casanueva, O, Hastings, J., Le Novere, N.

[International Worm Meeting, 2017]

C. elegans has recently been advanced as a premier metazoan model organism for the study of metabolism, with the publication of two whole-genome metabolic models (1, 2). Using these models together with -omics data allows the in-depth data-driven exploration of systems-level metabolism using in silico simulations. In a GENiE workshop to be held April 2017 at the Babraham Institute, Cambridge, UK, the relationships between these two existing metabolic models will be explored with the objective of generating a consensus model. Because the two reconstructions are still incomplete, and certain important pathways and areas of metabolism are currently under-annotated, we aim to identify specific areas that are relevant to the C. elegans community and prioritise them for further annotation in a follow-up community-driven "annotation jamboree" workshop. This poster will describe the main objectives set by the first workshop and opens the invitation to the C. elegans metabolic research community to contribute to the follow-up annotation efforts. 1. Gebauer, J.; Gentsch, C.; Mansfeld, J.; Schmei beta er, K.; Waschina, S.; Brandes, S.; Klimmasch, L.; Zamboni, N.; Zarse, K.; Schuster, S.; Ristow, M.; Schauble, S. & Kaleta, C. (2016), 'A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism.', Cell Syst 2(5), 312--322. 2. Yilmaz, L. S. & Walhout, A. J. M. (2016), 'A Caenorhabditis elegans Genome-Scale Metabolic Network Model.', Cell Syst 2(5), 297--311.

Kissoyan, K.A.B. et al. (2019) International Worm Meeting "Natural C. elegans Microbiota Protects against Infection via Production of a Cyclic Lipopeptide of the Viscosin Group."

Dierking, K., Kissoyan, K.A.B.

[International Worm Meeting, 2019]

C. elegans is associated in nature with a species-rich, distinct microbiota, which was characterized only recently [1]. Our understanding of C. elegans microbiota function is thus still in its infancy. Here, we identify natural C. elegans microbiota isolates of the Pseudomonas fluorescens subgroup that increase C. elegans resistance to pathogen infection. We show that different Pseudomonas isolates provide paramount protection from infection with the natural C. elegans pathogen Bacillus thuringiensis through distinct mechanisms [2] . The P. lurida isolates MYb11 and MYb12 (members of the P. fluorescens subgroup) protect C. elegans against B. thuringiensis infection by directly inhibiting growth of the pathogen both in vitro and in vivo. Using genomic and biochemical approaches, we demonstrate that MYb11 and MYb12 produce massetolide E, a cyclic lipopeptide biosurfactant of the viscosin group, which is active against pathogenic B. thuringiensis. In contrast to MYb11 and MYb12, P. fluorescens MYb115-mediated protection involves increased resistance without inhibition of pathogen growth and most likely depends on indirect, host-mediated mechanisms. We are currently investigating the molecular basis of P. fluorescens MYb115-mediated protection using a multi-omics approach to identify C. elegans candidate genes involved in microbiota-mediated protection. Moreover, we are further exploring the antagonistic interactions between C. elegans microbiota and pathogens. This work provides new insight into the functional significance of the C. elegans natural microbiota and expands our knowledge of immune-protective mechanisms. 1. Zhang, F., Berg, M., Dierking, K., Felix, M.A., Shapira, M., Samuel, B.S., and Schulenburg, H. (2017). Caenorhabditis elegans as a model for microbiome research. Front. Microbiol. 8:485. 2. Kissoyan, K.A.B., Drechsler, M., Stange, E.-L., Zimmermann, J., Kaleta, C., Bode, H.B., and Dierking, K. (2019). Natural C. elegans Microbiota Protects against Infection via Production of a Cyclic Lipopeptide of the Viscosin Group. Curr. Biol. 29.

Kissoyan KAB et al. (2019) Curr Biol "Natural C.elegans Microbiota Protects against Infection via Production of a Cyclic Lipopeptide of the Viscosin Group."

Dierking K, Kaleta C, Bode HB, Stange EL, Zimmermann J, Drechsler M, Kissoyan KAB

[Curr Biol, 2019]

Caenorhabditis elegans is associated in nature with a species-rich, distinct microbiota, which was characterized only recently [1]. Thus, our understanding of the relevance of the microbiota for nematode fitness is still at its infancy. One major benefit that the intestinal microbiota can provide to its host isprotection against pathogen infection [2]. However, the specific strains conferring the protection and the underlying mechanisms of microbiota-mediatedprotection are often unclear [3]. Here, we identify natural C.elegans microbiota isolates that increase C.elegans resistance to pathogen infection. We show that isolates of the Pseudomonas fluorescens subgroup provide paramount protection from infection with the natural pathogen Bacillus thuringiensis through distinct mechanisms. We found that the P.lurida isolates MYb11 and MYb12 (members of the P.fluorescens subgroup) protect C.elegans against B.thuringiensis infectionby directly inhibiting growth of the pathogen both invitro and invivo. Using genomic and biochemical analyses, we further demonstrate that MYb11 and MYb12 produce massetolide E, acyclic lipopeptide biosurfactant of the viscosin group [4, 5], which isactive against pathogenic B.thuringiensis. In contrast to MYb11 and MYb12, P.fluorescens MYb115-mediated protection involves increased resistance without inhibition of pathogen growth and most likely depends on indirect, host-mediated mechanisms. This work provides new insight intothe functional significance of the C.elegans natural microbiota and expands our knowledge of bacteria-derived compounds that can influence pathogen colonization in the intestine of an animal.

Yang, W. et al. (2017) International Worm Meeting "C. elegans microbiomics."

Leippe, M., Zimmermann, J., Obeng, N., Pees, B., Kaleta, C., Schulenburg, H., Yang, W., Aidley, J., Tholey, A., Cassidy, L., Kissoyan, K., Petersen, C., Dierking, K.

[International Worm Meeting, 2017]

The evolution of all higher organisms took place in the presence of microbes. Microbes may serve as food, act as competitors, commensals, or even interact with a host in a mutualistic form. Therefore, the naturally associated microbial interactors are key determinants of the biology of any organism. This also applies to C. elegans, even though the associated microbiome has been neglected in the numerous studies with this nematode. In fact, information on the worm's native microbiome was only published last year. Based on this knowledge, we here present a model for C. elegans and its interaction with naturally associated microbiome members of the genus Ochrobactrum. These bacteria are notable because of their ability to enter and persist in the nematode gut, even under stressful conditions. We explored the characteristics of this interaction at both phenotypic and molecular level, for the latter using a combination of different omics approaches and metabolic network analysis. Our results revealed an influence of the microbiome members on developmental processes, including development of the nervous system and sex-related traits, on reproduction, and also on ageing. These effects appear to be mediated by different transcription factors, including E-Box, GATA and SP transcription factors. In sum, our consideration of naturally associated microbiome members may help to develop a more realistic understanding of C. elegans life history and gene function.

Yang W et al. (2019) Front Microbiol "The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life."

Dirksen P, Waschina S, Petersen C, Kaleta C, Dierking K, Zimmermann J, Tholey A, Yang W, Leippe M, Schulenburg H, Pees B, Rosenstiel P

[Front Microbiol, 2019]

The biology of all organisms is influenced by the associated community of microorganisms. In spite of its importance, it is usually not well understood how exactly this microbiota affects host functions and what are the underlying molecular processes. To rectify this knowledge gap, we took advantage of the nematode <i>Caenorhabditis elegans</i> as a tractable, experimental model system and assessed the inducible transcriptome response after colonization with members of its native microbiota. For this study, we focused on two isolates of the genus <i>Ochrobactrum</i>. These bacteria are known to be abundant in the nematode's microbiota and are capable of colonizing and persisting in the nematode gut, even under stressful conditions. The transcriptome response was assessed across development and three time points of adult life, using general and <i>C. elegans</i>-specific enrichment analyses to identify affected functions. Our assessment revealed an influence of the microbiota members on the nematode's dietary response, development, fertility, immunity, and energy metabolism. This response is mainly regulated by a GATA transcription factor, most likely ELT-2, as indicated by the enrichment of (i) the GATA motif in the promoter regions of inducible genes and (ii) of ELT-2 targets among the differentially expressed genes. We compared our transcriptome results with a corresponding previously characterized proteome data set, highlighting a significant overlap in the differentially expressed genes, the affected functions, and ELT-2 target genes. Our analysis further identified a core set of 86 genes that consistently responded to the microbiota members across development and adult life, including several C-type lectin-like genes and genes known to be involved in energy metabolism or fertility. We additionally assessed the consequences of induced gene expression with the help of metabolic network model analysis, using a previously established metabolic network for <i>C. elegans</i>. This analysis complemented the enrichment analyses by revealing an influence of the <i>Ochrobactrum</i> isolates on <i>C. elegans</i> energy metabolism and furthermore metabolism of specific amino acids, fatty acids, and also folate biosynthesis. Our findings highlight the multifaceted impact of naturally colonizing microbiota isolates on <i>C. elegans</i> life history and thereby provide a framework for further analysis of microbiota-mediated host functions.

Dirksen P et al. (2020) G3 (Bethesda) "CeMbio - The Caenorhabditis elegans Microbiome Resource."

Zimmermann J, Assie A, Shapira M, Zhang F, Tietje AM, Marsh SA, Felix MA, Schulenburg H, Kaleta C, Dirksen P, Samuel BS

[G3 (Bethesda), 2020]

The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g. human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural <i>Caenorhabditis elegans</i> microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the <i>C. elegans</i> model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in <i>C. elegans</i>.

Zimmermann J et al. (2019) ISME J "The functional repertoire contained within the native microbiota of the model nematode Caenorhabditis elegans."

Bunk B, Schulenburg H, Yang W, Leippe M, Hoeppner MP, Zimmermann J, Sproer C, Aidley J, Obeng N, Pees B, Kaleta C, Dierking K, Kissoyan KA, Petersen C, Waschina S

[ISME J, 2019]

The microbiota is generally assumed to have a substantial influence on the biology of multicellular organisms. The exact functional contributions of the microbes are often unclear and cannot be inferred easily from 16S rRNA genotyping, which is commonly used for taxonomic characterization of bacterial associates. In order to bridge this knowledge gap, we here analyzed the metabolic competences of the native microbiota of the model nematode Caenorhabditis elegans. We integrated whole-genome sequences of 77 bacterial microbiota members with metabolic modeling and experimental characterization of bacterial physiology. We found that, as a community, the microbiota can synthesize all essential nutrients for C. elegans. Both metabolic models and experimental analyses revealed that nutrient context can influence how bacteria interact within the microbiota. We identified key bacterial traits that are likely to influence the microbe's ability to colonize C. elegans (i.e., the ability of bacteria for pyruvate fermentation to acetoin) and affect nematode fitness (i.e., bacterial competence for hydroxyproline degradation). Considering that the microbiota is usually neglected in C. elegans research, the resource presented here will help our understanding of this nematode's biology in a more natural context. Our integrative approach moreover provides a novel, general framework to characterize microbiota-mediated functions.

Zhao Y et al. (2007) BMC Genomics "Poly-G/poly-C tracts in the genomes of Caenorhabditis."

Zhao Y, O'Neil NJ, Rose AM

[BMC Genomics, 2007]

ABSTRACT: BACKGROUND: In the genome of Caenorhabditis elegans, homopolymeric poly-G/poly-C tracts (G/C tracts) exist at high frequency and are maintained by the activity of the DOG-1 protein. The frequency and distribution of G/C tracts in the genomes of C. elegans and the related nematode, C. briggsae were analyzed to investigate possible biological roles for G/C tracts. RESULTS: In C. elegans, G/C tracts are distributed along every chromosome in a non-random pattern. Most G/C tracts are within introns or are close to genes. Analysis of SAGE data showed that G/C tracts correlate with the levels of regional gene expression in C. elegans. G/C tracts are over-represented and dispersed across all chromosomes in another Caenorhabditis species, C. briggase. However, the positions and distribution of G/C tracts in C. briggsae differ from those in C. elegans. Furthermore, the C. briggsae dog-1 ortholog CBG19723 can rescue the mutator phenotype of C. elegans dog-1 mutants. CONCLUSIONS: The abundance and genomic distribution of G/C tracts in C. elegans, the effect of G/C tracts on regional transcription levels, and the lack of positional conservation of G/C tracts in C. briggsae suggest a role for G/C tracts in chromatin structure but not in the transcriptional regulation of specific genes.

Bhagwati P Gupta et al. (2002) West Coast Worm Meeting "Genetic analysis of the vulval mutants in C. briggsae"

Shahla Gharib, Bhagwati P Gupta, Paul W Sternberg, Jennifer X Li

[West Coast Worm Meeting, 2002]

To understand the evolution of developmental mechanisms, we are doing a comparative analysis of vulval patterning in C. elegans and C. briggsae. C. briggsae is closely related to C. elegans and has identical looking vulval morphology. However, recent studies have indicated subtle differences in the underlying mechanisms of development. The recent completion of C. briggsae genome sequence by the C. elegans Sequencing Consortium is extremely valuable in identifying the conserved genes between C. elegans and C. briggsae.

Antika TR et al. (2023) J Biol Chem "Sequence-specific targeting of C. elegans C-Ala to the D-loop of tRNAAla."

Horng JC, Hsu HL, Nazilah KR, Wang CC, Wang TL, Wang SC, Antika TR, Chuang TH, Chrestella DJ, Wang SW, Tseng YK, Pan HC

[J Biol Chem, 2023]

Alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout its biology. Nevertheless, its C-terminal domain (C-Ala) is highly diverged and has been shown to play a role in either tRNA or DNA binding. Interestingly, we discovered that Caenorhabditis elegans cytoplasmic C-Ala (Ce-C-Ala_c) robustly binds both ligands. How Ce-C-Ala_c targets its cognate tRNA and whether a similar feature is conserved in its mitochondrial counterpart remain elusive. We show that the N- and C-terminal subdomains of Ce-C-Ala_c are responsible for DNA and tRNA binding, respectively. Ce-C-Ala_c specifically recognized the conserved invariant base G¹⁸ in the D-loop of tRNA^Ala through a highly conserved lysine residue, K934. Despite bearing little resemblance to other C-Ala domains, C. elegans mitochondrial C-Ala (Ce-C-Ala_m) robustly bound both tRNA^Ala and DNA and maintained targeting specificity for the D-loop of its cognate tRNA. This study uncovers the underlying mechanism of how C. elegans C-Ala specifically targets the D-loop of tRNA^Ala.