Tracey KJ (2011) Science "Cell biology. Ancient neurons regulate immunity."

Tracey KJ

[Science, 2011]

Tracey KJ (2015) Cold Spring Harb Perspect Biol "Approaching the next revolution? Evolutionary integration of neural and immune pathogen sensing and response."

Tracey KJ

[Cold Spring Harb Perspect Biol, 2015]

Mammalian immunity evolved by the process of natural selection that produced differential survival and reproduction advantages through combinations of hereditary traits underlying the response to pathogens. Primitive animals sense the presence of microbial pathogens through recognition of pathogen-derived molecules in their rudimentary immune and nervous systems. No molecular biological mechanism assigns primacy of pathogen sensing mechanisms to immune cells over neurons. Rather, in animals as diverse as Caenorhabditis elegans to mammals, neural reflexes are activated by the presence of pathogens and transduce neural mechanisms that control the development of immunity. A coming revolution in immunological thinking will require immunologists to incorporate neural circuits into understanding pathogen signal transduction, and the molecular mechanisms of learning, that culminate in immunity.

Tracey M Small et al. (2002) East Coast Worm Meeting "A new isoform of UNC-89 with two MLCK-like protein kinase domains"

Denise B Flaherty, Guy M Benian, Tracey M Small, Mark Borodovsky, Kristina B Mercer, Teresa M Williams

[East Coast Worm Meeting, 2002]

Mutants in the C. elegans gene unc-89 have disorganized myofibrils in which thick filaments are not organized into A-bands, and for most alleles, there are no M-lines. unc-89 encodes a giant 732,000 Da polypeptide that is a member of the intracellular branch of the Ig superfamily (Benian et al., 1996). UNC-89 is composed of 53 Ig domains and several signal transduction domains, including a dbl-homology (DH) domain near its N-terminus. Recently, a possible human analog of UNC-89 called "obscurin" has been identified (Young et al., 2001). Teichmann and Chothia (2000) and WormBase predicted that gene C24G7.5 encodes an Ig superfamily member that is expressed in muscle. The predicted initiator methionine codon for C24G7.5 is only 2.7 kb downstream of the 3' end of unc-89. With a combination of GeneMark.hmm exon predictions and RT-PCR, we have been able to demonstrate that C24G7.5 is not a separate gene, but rather a set of alternatively spliced exons for unc-89. Splicing treats the 680 bp 3'UTR and stop codon of the previous unc-89 as an intron, and continues into the C24G7.5 exons. Whereas the previously characterized UNC-89 (UNC-89-S) is 6,632 residues, the new isoform (UNC-89-L) is potentially 8,082 residues. The C-terminal extension of UNC-89-L contains a protein kinase, 640 residues of low sequence complexity, an Ig, a Fn3, and a second protein kinase domain. The two kinase domains of UNC-89-L have highest homology to twitchin, MLCKs, and titin, especially in the large subunit. However, they show significant dissimilarity in subdomains I and II that suggest that both kinase domains might lack phosphotransferase activity. Using RT-PCR we can show that both kinase domains are included in an UNC-89-L polypeptide.

Tracey M Small et al. (2005) International Worm Meeting "unc-89 is a complex gene with three promoters that direct expression of at least six major isoforms."

Mark Borodovsky, Guy M Benian, Tracey M Small, Kim M Gernert

[International Worm Meeting, 2005]

unc-89 mutants display disorganized muscle A-bands, and usually, lack of M-lines. Antibodies raised to 3 different regions of UNC-89 proteins localize to the M-line region of body wall muscle, and to the middle of pharyngeal and anal depressor single sarcomere muscles. The unc-89 gene encodes at least 6 major isoforms: UNC-89-A (original isoform, 732 kDa); UNC-89-B (potentially 900 kDa), the protein predicted if all exons are used in the same transcript; UNC-89-E and UNC-89F, which are identical to A and B, respectively, minus the KSP region; UNC-89-C and UNC-89-D (each 156 kDa), which, except for unique N-terminal tails of 8 and 11 residues, respectively, are identical to the C-terminus of UNC-89-B. unc-89 contains at least 3 promoters: one directing expression of UNC-89-A, B, -E, and -F primarily in body-wall and pharyngeal muscle, one internal promoter directing expression of UNC-89-C primarily in body-wall muscle, and one internal promoter directing expression of UNC-89-D primarily in the enteric muscles. All 3 promoters also express in vulval muscle. Most of these new isoforms contain two protein kinase domains, of the myosin light chain kinase (MLCK) family. UNC-89-B and F contain two complete protein kinase domains, PK1 and PK2. UNC-89-C and D begin with partial kinase domains, designated PK1-C and PK1-D. Homology modeling suggests that PK2 is catalytically active, and PK1 is inactive. Furthermore, modeling shows that PK1-C and PK1-D consist of a C-terminal large lobe, a hinge region and a -turn- structure. Yeast 2-hybrid screens are being conducted to determine the substrates and/or binding partners of the whole and partial kinase domains. We have confirmed that the intragenic deletions of the kinase domains made for us by the C. elegans knockout project (tm752 and ok1116) result in a complete lack of UNC-89-C and D proteins by western blot. We also noticed that these isoforms are lacking in the st79 mutant, which led us to sequence the 5 kb of new unc-89 coding sequence of this allele. We found the mutation to be a G to A change that results in a stop codon within the 5th exon from the 3 end of unc-89- B, -C, -D and -F. tm752 and st79 show reduced motility and abnormal body wall muscle structure, but no pharyngeal muscle defects. Moreover, they lack detectable large kinase domain-containing isoforms, -B and -F. Thus, although we have shown by our promoter analysis and antibody staining that the large kinase domain-containing isoforms, -B and F, are expressed in pharyngeal muscle, they are apparently not required for pharyngeal muscle structure.

DePellegrin Connelly, Tracey et al. (2009) International Worm Meeting "GENETICS, the peer-edited journal of the Genetics Society of America, reports on updates and special projects, including article links to WormBase."

DePellegrin Connelly, Tracey, Schedl, Tim

[International Worm Meeting, 2009]

GENETICS, the peer-edited journal of the Genetics Society of America has partnered with WormBase (Arun Rangarajan, Hans-Michael Muller and Paul Sternberg) to produce interactive journal articles (in full text/HTML, XML and PDF outputs). A reader who clicks on a gene or protein name, allele, transgene (or potentially any object found in the database) is taken directly to the corresponding page in WormBase. This innovative project integrates two major modes of communication used in the biological sciences: journal articles and databases. The project offers several benefits to readers, including fast access to relevant information associated with a genetic object in the text. This information can be general, providing an overview (e.g. gene summary), or highly specific, providing an important experimental detail (e.g. the molecular lesion of an allele). Also, the project promotes standardization of individual object nomenclature (e.g. gene names) and simplifies connections when there is a nomenclature change. Finally, the objects remain connected but evolve with advancesin knowledge. The benefits to WormBase include increased use of and interest in the database, more efficient and extensive corrections of information in the database by the community, facile incorporation of new information, reverse integration of the database with the primary data in the literature, all with minimal ongoing cost. We will show examples of the article links to WormBase, and discuss a number of other initiatives being undertaken by the journal GENETICS.

Gonzalez de la Rosa PM et al. (2021) G3 (Bethesda) "A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes."

Thomson M, Tracey A, Gonzalez de la Rosa PM, Blaxter M, Trivedi U, Tandonnet S

[G3 (Bethesda), 2021]

Eukaryotic chromosomes have phylogenetic persistence. In many taxa, each chromosome has a single functional centromere with essential roles in spindle attachment and segregation. Fusion and fission can generate chromosomes with no or multiple centromeres, leading to genome instability. Groups with holocentric chromosomes (where centromeric function is distributed along each chromosome) might be expected to show karyotypic instability. This is generally not the case, and in Caenorhabditis elegans, it has been proposed that the role of maintenance of a stable karyotype has been transferred to the meiotic pairing centers, which are found at one end of each chromosome. Here, we explore the phylogenetic stability of nematode chromosomes using a new telomere-to-telomere assembly of the rhabditine nematode Oscheius tipulae generated from nanopore long reads. The 60-Mb O. tipulae genome is resolved into six chromosomal molecules. We find the evidence of specific chromatin diminution at all telomeres. Comparing this chromosomal O. tipulae assembly with chromosomal assemblies of diverse rhabditid nematodes, we identify seven ancestral chromosomal elements (Nigon elements) and present a model for the evolution of nematode chromosomes through rearrangement and fusion of these elements. We identify frequent fusion events involving NigonX, the element associated with the rhabditid X chromosome, and thus sex chromosome-associated gene sets differ markedly between species. Despite the karyotypic stability, gene order within chromosomes defined by Nigon elements is not conserved. Our model for nematode chromosome evolution provides a platform for investigation of the tensions between local genome rearrangement and karyotypic evolution in generating extant genome architectures.

Stevens L et al. (2022) Genome Biol Evol "Chromosome-level reference genomes for two strains of Caenorhabditis briggsae: an improved platform for comparative genomics."

Dekker J, Moya ND, Chitrakar R, Tanny RE, Andersen EC, Baugh LR, Walhout AJM, Stevens L, Gibson SB, Na H, Tracey A

[Genome Biol Evol, 2022]

The publication of the Caenorhabditis briggsae reference genome in 2003 enabled the first comparative genomics studies between C. elegans and C. briggsae, shedding light on the evolution of genome content and structure in the Caenorhabditis genus. However, despite being widely used, the currently available C. briggsae reference genome is substantially less complete and structurally accurate than the C. elegans reference genome. Here, we used high-coverage Oxford Nanopore long-read and chromosome conformation capture data to generate chromosome-level reference genomes for two C. briggsae strains: QX1410, a new reference strain closely related to the laboratory AF16 strain, and VX34, a highly divergent strain isolated in China. We also sequenced 99 recombinant inbred lines (RILs) generated from reciprocal crosses between QX1410 and VX34 to create a recombination map and identify chromosomal domains. Additionally, we used both short- and long-read RNA sequencing (RNA-seq) data to generate high-quality gene annotations. By comparing these new reference genomes to the current reference, we reveal that hyper-divergent haplotypes cover large portions of the C. briggsae genome, similar to recent reports in C. elegans and C. tropicalis. We also show that the genomes of selfing Caenorhabditis species have undergone more rearrangement than their outcrossing relatives, which has biased previous estimates of rearrangement rate in Caenorhabditis. These new genomes provide a substantially improved platform for comparative genomics in Caenorhabditis and narrow the gap between the quality of genomic resources available for C. elegans and C. briggsae.

Foster JM et al. (2020) Nat Commun "Sex chromosome evolution in parasitic nematodes of humans."

Rogers MB, Tsai YC, Michalski ML, Grote A, Chung M, Tracey A, Ghedin E, Geber A, Foster JM, Libro S, Welch L, Cotton JA, Paulini M, Twaddle A, Korlach J, Lustigman S, Teigen L, Berriman M, Li Y, Holroyd N, Mattick J, Dunning Hotopp JC, Clark TA

[Nat Commun, 2020]

Sex determination mechanisms often differ even between related species yet the evolution of sex chromosomes remains poorly understood in all but a few model organisms. Some nematodes such as Caenorhabditis elegans have an XO sex determination system while others, such as the filarial parasite Brugia malayi, have an XY mechanism. We present a complete B. malayi genome assembly and define Nigon elements shared with C. elegans, which we then map to the genomes of other filarial species and more distantly related nematodes. We find a remarkable plasticity in sex chromosome evolution with several distinct cases of neo-X and neo-Y formation, X-added regions, and conversion of autosomes to sex chromosomes from which we propose a model of chromosome evolution across different nematode clades. The phylum Nematoda offers a new and innovative system for gaining a deeper understanding of sex chromosome evolution.

Doyle SR et al. (2020) Commun Biol "Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm."

Berriman M, Devaney E, Salle G, Laing R, Britton C, Sargison N, Gilleard JS, Beech R, Shabbir MZ, Doyle SR, Noonan JD, Quail MA, Martinelli A, Beasley H, Howe KL, Holroyd N, Redman E, Wit J, Bartley D, Rodgers FH, Bazant W, Sankaranarayanan G, Cotton JA, Chaudhry U, Paulini M, Maitland K, Tracey A, Brooks K

[Commun Biol, 2020]

Haemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants and has become a key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Here, we report using PacBio long-read and OpGen and 10X Genomics long-molecule methods to generate a highly contiguous 283.4 Mbp chromosome-scale genome assembly including a resolved sex chromosome for the MHco3(ISE).N1 isolate. We show a remarkable pattern of conservation of chromosome content with Caenorhabditis elegans, but almost no conservation of gene order. Short and long-read transcriptome sequencing allowed us to define coordinated transcriptional regulation throughout the parasite's life cycle and refine our understanding of cis- and trans-splicing. Finally, we provide a comprehensive picture of chromosome-wide genetic diversity both within a single isolate and globally. These data provide a high-quality comparison for understanding the evolution and genomics of Caenorhabditis and other nematodes and extend the experimental tractability of this model parasitic nematode in understanding helminth biology, drug discovery and vaccine development, as well as important adaptive traits such as drug resistance.

Foth BJ et al. (2014) Nat Genet "Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction."

Cooper PJ, Nichol S, Zarowiecki M, Huckvale T, Liu JZ, Berriman M, Cotton JA, Grencis RK, Foth BJ, Reid AJ, Bancroft AJ, Stanley EJ, Tsai IJ, Holroyd N, Tracey A

[Nat Genet, 2014]

Whipworms are common soil-transmitted helminths that cause debilitating chronic infections in man. These nematodes are only distantly related to Caenorhabditis elegans and have evolved to occupy an unusual niche, tunneling through epithelial cells of the large intestine. We report here the whole-genome sequences of the human-infective Trichuris trichiura and the mouse laboratory model Trichuris muris. On the basis of whole-transcriptome analyses, we identify many genes that are expressed in a sex- or life stage-specific manner and characterize the transcriptional landscape of a morphological region with unique biological adaptations, namely, bacillary band and stichosome, found only in whipworms and related parasites. Using RNA sequencing data from whipworm-infected mice, we describe the regulated T helper 1 (TH1)-like immune response of the chronically infected cecum in unprecedented detail. In silico screening identified numerous new potential drug targets against trichuriasis. Together, these genomes and associated functional data elucidate key aspects of the molecular host-parasite interactions that define chronic whipworm infection.