Smith MJ (1992) DNA Seq "A C. elegans gene encodes a protein homologous to mammalian calreticulin."

Smith MJ

[DNA Seq, 1992]

The gene encoding a C. elegans homologue of the mammalian reticuloplasmin, calreticulin, was cloned and sequenced and the amino-acid sequence of its product deduced. The coding region of the gene comprises three exons separated by introns of 95 and 55 nucleotides, followed by either 158 or 279 bases of 3' non-coding sequence before putative polyadenylation signals. The precursor protein of 395 residues includes an N-terminal signal sequence of 13 residues. The C-terminus has the ER retention signal HDEL preceded by a polyacidic zone similar to known mammalian calreticulins. The sequence shows a 61% identity with mouse calreticulin, increasing to 82% in the proline-rich region of the molecule. Comparison of the C. elegans sequence with the calreticulin-related antigen RAL-1 of Oncocerca volvulus shows 73% identity, excluding the calreticulin C-terminal region. The sequence of this region differs markedly from RAL-1 where the parasite protein has a polybasic stretch and no ER retention signal. The C. elegans gene described here and designated crt-1 was mapped to a region towards the left-hand end of Chromosome V on the physical map of the genome. Southern blotting of genomic DNA indicates that in C. elegans the calreticulin homologue exists in only one form as the product of a single gene.

Bichai F et al. (2009) Water Res "Protection against UV disinfection of E. coli bacteria and B. subtilis spores ingested by C. elegans nematodes."

Barbeau B, Bichai F, Payment P

[Water Res, 2009]

Nematodes, which occur abundantly in granular media filters of drinking water treatment plants and in distribution systems, can ingest and transport pathogenic bacteria and provide them protection against chemical disinfectants. However, protection against UV disinfection had not been investigated to date. In this study, Caenorhabditis elegans nematodes (wild-type strain N2) were allowed to feed on Escherichia coli OP50 and Bacillus subtilis spores before being exposed to 5 and 40 mJ/cm(2) UV fluences, using a collimated beam apparatus (LP, 254 nm). Sonication (15 W, 60s) was used to extract bacteria from nematode guts following UV exposure in order to assess the amount of ingested bacteria that resisted the UV treatment using a standard culture method. Bacteria located inside the gut of C. elegans were shown to benefit from a significant protection against UV. Approximately 15% of the applied UV fluence of 40 mJ/cm(2) (as typically used in WTP) was found to reach the bacteria located inside nematode guts based on the inactivation of recovered bacteria (2.7 log reduction of E. coli bacteria and 0.7 log reduction of B. subtilis spores at 40 mJ/cm(2)). To our knowledge, this study is the first demonstration of the protection effect of bacterial internalization by higher organisms against UV treatment, using the specific case of E. coli and B. subtilis spores ingested by C. elegans.

Goedert M et al. (1996) J Cell Sci "PTL-1, a microtubule-associated protein with tau-like repeats from the nematode Caenorhabditis elegans."

Smith MJ, Hasegawa M, Ahringer JA, Goedert M, Jakes R, Spillant MG, Hill F, Baur CP

[J Cell Sci, 1996]

Tau, MAP2 and MAP4 are structural microtubule-associated proteins (MAPs) that promote the assembly and stability of microtubules. They share three or four imperfect tandem repeats of an amino acid motif, which is involved in the binding to microtubules. All sequences to data containing this motif are of mammalian origin. We report here the cloning and functional characterisation of a new member of this family of proteins from the nematode Caenorhabditis elegans. This protein exists as two isoforms of 413 and 453 amino acids with four or five tandem repeats that are 50% identical to the tau/MAP2/MAP4 repeats. Both isoforms bind to microtubules and promote microtubule assembly, with the five-repeat isoform being more effective at promoting assembly than the four-repeat isoform. When expressed in COS cells, the five-repeat isoform co-localises with microtubules and induces the formation of microtubule bundles, whereas its expression in Sf9 cells leads to the extension of long unipolar processes. In view of its length, amino acid sequence and functional characteristics, we have named this invertebrate structural MAP 'Protein with Tau-Like Repeats' (PTL-1). In C. elegans PTL-1 is expressed in two places known to require microtubule function. It is first seen in the embryonic epidermis, when circumferentially oriented microtubules help to distribute forces generated during elongation. Later, it is found in mechanosensory neurons which contain unusual 15 protofilament microtubules required for the response to touch. These findings indicate that MAPs of the tau/MAP2/MAP4 family are found throughout much of the animal kingdom, where they may play a role in specialised processes requiring microtubules.

Bo S et al. (2019) J Theor Biol "Potential relations between post-spliced introns and mature mRNAs in the Caenorhabditis elegans genome."

Zhao X, Li H, Bao T, Zhang Q, Lu Z, Bo S

[J Theor Biol, 2019]

There are potential interactions between introns and their corresponding coding sequences (CDSs) in ribosomal protein genes that have been proposed by our group and the interactions are achieved by sequence matches between the two kinds of sequences. Here, the optimal matching relations between mature mRNAs and their corresponding introns in Caenorhabditis elegans (C.elegans) were investigated by improved Smith-Waterman local alignment software. Our results showed that the remarkably matched regions appear in the untranslated regions (UTRs) of mRNAs, especially in the 3' UTR. The optimal matched segments (OMSs) are highly organized segments. In addition, the optimal matching relations were analysed between mature mRNAs and other introns. The matching strengths in the UTRs are clearly lower than those in their corresponding introns. Our studies indicate that there are potential interactions between mature mRNAs and their corresponding introns and the post-spliced introns should have other novel functions in the gene expression process.

Cohn DH et al. (2003) Am J Hum Genet "Mental retardation and abnormal skeletal development (Dyggve-Melchior-Clausen dysplasia) due to mutations in a novel, evolutionarily conserved gene."

Ehtesham N, Shanske A, Cohn DH, Krakow D, Powell BR, Rimoin DL, Unger S, Reinker K

[Am J Hum Genet, 2003]

Dyggve-Melchior-Clausen dysplasia (DMC) and Smith-McCort dysplasia (SMC) are similar, rare autosomal recessive osteochondrodysplasias. The radiographic features and cartilage histology in DMC and SMC are identical. However, patients with DMC exhibit significant developmental delay and mental retardation, the major features that distinguish the two conditions. Linkage studies localized the SMC and DMC disease genes to chromosome 18q12-21.1, providing evidence suggesting that they are allelic disorders. Sequence analysis of the coding exons of the FLJ90130 gene, a highly evolutionarily conserved gene within the recombination interval defined in the linkage study, identified mutations in SMC and DMC patients. The affected individuals in two consanguinous DMC families were homozygous for a stop codon mutation and a frameshift mutation, respectively, demonstrating that DMC represents the FLJ90130-null phenotype. The data confirm the hypothesis that SMC and DMC are allelic disorders and identify a gene necessary for normal skeletal development and brain function.

Boateng R et al. (2018) Genetics "New Role for an Old Protein: An Educational Primer for Use with "The Identification of a Novel Mutant Allele of topoisomerase II in Caenorhabditis elegans Reveals a Unique Role in Chromosome Segregation During Spermatogenesis"."

Allen AK, Boateng R

[Genetics, 2018]

Modern experimental techniques, such as whole-genome sequencing and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 endogenous genome editing, are enabling researchers to identify and further characterize the roles of proteins that were previously thought of as well defined. In the December 2016 issue of GENETICS, an article by Jaramillo-Lambert et al. identified a new role for the enzyme topoisomerase II in Caenorhabditis elegans male meiosis. This Primer article is designed to provide essential background information on C. elegans spermatogenesis and the relevant scientific techniques that will assist students and instructors in their understanding and discussion of the related article.Related article in GENETICS: Jaramillo-Lambert, A., A. S. Fabritius A. S., T. J. Hansen T. J., H. E. Smith H. E., and A. Golden A., 2016The identification of a novel mutant allele of topoisomerase II in Caenorhabditis elegans reveals a unique role in chromosome segregation during spermatogenesis. Genetics204: 1407-1422.

Ehtesham N et al. (2002) Am J Hum Genet "Evidence that Smith-McCort dysplasia and Dyggve-Melchior-Clausen dysplasia are allelic disorders that result from mutations in a gene on chromosome 18q12."

Cohn DH, Shanske A, King LM, Unger S, Ehtesham N, Powell BR, Cantor RM, Rimoin DL, Reinker K

[Am J Hum Genet, 2002]

Smith-McCort dysplasia is a rare autosomal recessive osteochondrodysplasia characterized by short limbs and a short trunk with a barrel-shaped chest. The radiographic phenotype includes platyspondyly, generalized abnormalities of the epiphyses and metaphyses, and a distinctive lacy appearance of the iliac crest. We performed a genomewide scan in a consanguineous family from Guam and found evidence of linkage to loci on chromosome 18q12. Analysis of a second, smaller family was also consistent with linkage to this region, producing a maximum combined two-point LOD score of 3.04 at a recombination fraction of 0 for the marker at locus D18S450. A 10.7-cM region containing the disease gene was defined by recombination events in two affected individuals in the larger family. Furthermore, all affected children in the larger family were homozygous for a subset of marker loci within this region, defining a 1.5-cM interval likely to contain the defective gene. Analysis of three small, unrelated families with Dyggve-Melchior-Clausen syndrome, a radiographically identical disorder with the additional clinical finding of mental retardation, provided evidence of linkage to the same region, a result consistent with the hypothesis that the two disorders are allelic.

Shaham S (2009) PLoS One "galign: a tool for rapid genome polymorphism discovery."

Shaham S

[PLoS One, 2009]

BACKGROUND: Highly parallel sequencing technologies have become important tools in the analysis of sequence polymorphisms on a genomic scale. However, the development of customized software to analyze data produced by these methods has lagged behind. METHODS/PRINCIPAL FINDINGS: Here I describe a tool, 'galign', designed to identify polymorphisms between sequence reads obtained using Illumina/Solexa technology and a reference genome. The 'galign' alignment tool does not use Smith-Waterman matrices for sequence comparisons. Instead, a simple algorithm comparing parsed sequence reads to parsed reference genome sequences is used. 'galign' output is geared towards immediate user application, displaying polymorphism locations, nucleotide changes, and relevant predicted amino-acid changes for ease of information processing. To do so, 'galign' requires several accessory files easily derived from an annotated reference genome. Direct sequencing as well as in silico studies demonstrate that 'galign' provides lesion predictions comparable in accuracy to available prediction programs, accompanied by greater processing speed and more user-friendly output. We demonstrate the use of 'galign' to identify mutations leading to phenotypic consequences in C. elegans. CONCLUSION/SIGNIFICANCE: Our studies suggest that 'galign' is a useful tool for polymorphism discovery, and is of immediate utility for sequence mining in C. elegans.

Evan Johnson W et al. (2011) Biometrics "Dynamic linear model for the identification of miRNAs in next-generation sequencing data."

Evan Johnson W, Bass BL, Welker NC

[Biometrics, 2011]

Next-generation sequencing technologies are poised to revolutionize the field of biomedical research. The increased resolution of these data promise to provide a greater understanding of the molecular processes that control the morphology and behavior of a cell. However, the increased amounts of data require innovative statistical procedures that are powerful while still being computationally feasible. In this article, we present a method for identifying small RNA molecules, called miRNAs, which regulate genes by targeting their mRNAs for degradation or translational repression. In the first step of our modeling procedure, we apply an innovative dynamic linear model that identifies candidate miRNA genes in high-throughput sequencing data. The model is flexible and can accurately identify interesting biological features while accounting for both the read count, read spacing, and sequencing depth. Additionally, miRNA candidates are also processed using a modified Smith-Waterman sequence alignment that scores the regions for potential RNA hairpins, one of the defining features of miRNAs. We illustrate our method on simulated datasets as well as on a small RNACaenorhabditis elegansdataset from the Illumina sequencing platform. These examples show that our method is highly sensitive for identifying known and novel miRNA genes.

Steinfeld JB et al. (2019) Genes Dev "Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination."

Boulton SJ, Rothstein R, Symington LS, Al-Zain A, Qi Z, Kwon Y, Smith MJ, Steinfeld JB, Crickard JB, Belan O, Terakawa T, Sung P, Greene EC, Zhao W

[Genes Dev, 2019]

The vast majority of eukaryotes possess two DNA recombinases: Rad51, which is ubiquitously expressed, and Dmc1, which is meiosis-specific. The evolutionary origins of this two-recombinase system remain poorly understood. Interestingly, Dmc1 can stabilize mismatch-containing base triplets, whereas Rad51 cannot. Here, we demonstrate that this difference can be attributed to three amino acids conserved only within the Dmc1 lineage of the Rad51/RecA family. Chimeric Rad51 mutants harboring Dmc1-specific amino acids gain the ability to stabilize heteroduplex DNA joints with mismatch-containing base triplets, whereas Dmc1 mutants with Rad51-specific amino acids lose this ability. Remarkably, RAD-51 from <i>Caenorhabditis elegans</i>, an organism without Dmc1, has acquired &quot;Dmc1-like&quot; amino acids. Chimeric <i>C. elegans</i> RAD-51 harboring &quot;canonical&quot; Rad51 amino acids gives rise to toxic recombination intermediates, which must be actively dismantled to permit normal meiotic progression. We propose that Dmc1 lineage-specific amino acids involved in the stabilization of heteroduplex DNA joints with mismatch-containing base triplets may contribute to normal meiotic recombination.