Joshi CJ et al. (2022) PLoS Comput Biol "What are housekeeping genes?"

Lewis NE, O'Rourke EJ, Drangowska-Way A, Ke W, Joshi CJ

[PLoS Comput Biol, 2022]

The concept of "housekeeping gene" has been used for four decades but remains loosely defined. Housekeeping genes are commonly described as "essential for cellular existence regardless of their specific function in the tissue or organism", and "stably expressed irrespective of tissue type, developmental stage, cell cycle state, or external signal". However, experimental support for the tenet that gene essentiality is linked to stable expression across cell types, conditions, and organisms has been limited. Here we use genome-scale functional genomic screens together with bulk and single-cell sequencing technologies to test this link and optimize a quantitative and experimentally validated definition of housekeeping gene. Using the optimized definition, we identify, characterize, and provide as resources, housekeeping gene lists extracted from several human datasets, and 10 other animal species that include primates, chicken, and C. elegans. We find that stably expressed genes are not necessarily essential, and that the individual genes that are essential and stably expressed can considerably differ across organisms; yet the pathways enriched among these genes are conserved. Further, the level of conservation of housekeeping genes across the analyzed organisms captures their taxonomic groups, showing evolutionary relevance for our definition. Therefore, we present a quantitative and experimentally supported definition of housekeeping genes that can contribute to better understanding of their unique biological and evolutionary characteristics.

Joshi PM et al. (2005) Curr Biol "Nematode gastrulation: having a BLASTocoel!"

Rothman JH, Joshi PM

[Curr Biol, 2005]

During gastrulation of the nematode worm Caenorhabditis elegans, individual cells ingress into a solid ball of cells. Gastrulation in a basal nematode, in contrast, has now been found to occur by invagination into a blastocoel, revealing an unanticipated embryological affinity between nematodes and all other triploblastic metazoans.

Joshi A et al. (1989) Folia Parasitol (Praha) "Brugia malayi: status of host during different stages of infection."

Ghatak S, Saxena JK, Joshi A, Sen AB, Murthy PK

[Folia Parasitol (Praha), 1989]

The status of glycogen, protein, lipid components, lipid peroxides and a few enzymes of energy metabolism was studied in liver of Mastomys natalensis during the development of Brugia malayi infection. Glycogen and lipid contents were decreased during the patent phase of infection while total protein was slightly altered in latent animals. Phospholipid and triglyceride contents declined at prepatent and patent phase of infection. The levels of lactate and malate dehydrogenases, as well as of adenosine triphosphatases (Na+K+, Mg2+, Ca2+), were significantly elevated and monoamine oxidase activity was decreased at patent phase of infection, while succinic dehydrogenase remained unaltered. The lipid peroxide formation was enhanced in liver during the development of filarial infection.

Joshi PM et al. (2010) Dev Dyn "Caenorhabditis elegans as a model for stem cell biology."

Rothman JH, Riddle MR, Djabrayan NJ, Joshi PM

[Dev Dyn, 2010]

We review the application of Caenorhabditis elegans as a model system to understand key aspects of stem cell biology. The only bona fide stem cells in C. elegans are those of the germline, which serves as a valuable paradigm for understanding how stem-cell niches influence maintenance and differentiation of stem cells and how somatic differentiation is repressed during germline development. Somatic cells that share stem cell-like characteristics also provide insights into principles in stem-cell biology. The epidermal seam cell lineages lend clues to conserved mechanisms of self-renewal and expansion divisions. Principles of developmental plasticity and reprogramming relevant to stem-cell biology arise from studies of natural transdifferentiation and from analysis of early embryonic progenitors, which undergo a dramatic transition from a pluripotent, reprogrammable condition to a state of committed differentiation. The relevance of these developmental processes to our understanding of stem-cell biology in other organisms is discussed.

Joshi M et al. (2024) MicroPubl Biol "mNeonGreen aggregates when overexpressed in C. elegans neurons."

van Falier SJA, Joshi M, Sinnige T

[MicroPubl Biol, 2024]

The optical transparency of the nematode <i>Caenorhabditis elegans</i> makes it possible to monitor the behaviour of fluorescently labelled proteins in a living multicellular organism. This study investigates the suitability of mNeonGreen as a fluorescent tag for studying proteins of interest in the nervous system of adult <i>C. elegans</i> . Despite its reported brightness, stability, and monomeric nature, our findings reveal that mNeonGreen forms solid aggregates in <i>C. elegans</i> neurons, particularly upon plasmid overexpression. We anticipate that this property may lead to artefacts when analysing for example the subcellular distribution or turnover of a tagged protein of interest.

Pradeep M Joshi et al. (2005) International Worm Meeting "An RNAi screen of CED-4 dependent sterile genes."

Niels Holten-Andersen, Benjamin Youngblood, Joel H Rothman, Pradeep M Joshi

[International Worm Meeting, 2005]

Apoptosis, or PCD, plays a vital role in development and homeostasis. Inappropriate PCD regulation has been linked to many human diseases including neurodegenerative and autoimmune diseases. Genetic analyses have identified an evolutionarily conserved core apoptotic pathway. However, identification of PCD regulators in multiple genome-wide RNAi screens suggests that regulation of PCD in C. elegans is more complex than previously thought [1-6]. Specifically, RNAi of the apoptotic suppressors icd-1 and -2 results in CED-4-dependent, CED-3-independent PCD and sterility [4]. To identify additional PCD regulators, we are screening for CED-4-dependent sterile genes. Genes that when inhibited by RNAi result in a significant increase in fecundity in a ced-4(-) background compared to N2 will be characterized for cell death, proliferation and differentiation defects. To date, we have found that of 160 genes that result in sterility by RNAi, 32 are suppressible to some degree by ced-4(n1162). The results of the screen and detailed analysis of candidate genes that show the strongest effect will be presented. 1.Lettre, G., et al., Genome-wide RNAi identifies p53-dependent and -independent regulators of germ cell apoptosis in C. elegans. Cell Death Differ, 2004. 11(11): p. 1198-203. 2.Parrish, J., et al., Mitochondrial endonuclease G is important for apoptosis in C. elegans. Nature, 2001. 412(6842): p. 90-4. 3.Parrish, J.Z., et al., Functional genomic analysis of apoptotic DNA degradation in C. elegans. Mol Cell, 2003. 11(4): p. 987-96. 4.Bloss, T.A., et al., Suppression of CED-3-independent apoptosis by mitochondrial betaNAC in Caenorhabditis elegans. Nature, 2003. 424(6952): p. 1066-71. 5.Derry, W.B., et al., Caenorhabditis elegans p53: role in apoptosis, meiosis, and stress resistance. Science, 2001. 294(5542): p. 591-5. 6.Schumacher, B., et al., The C. elegans homolog of the p53 tumor suppressor is required for DNA damage-induced apoptosis. Curr Biol, 2001. 11(21): p. 1722-7.

Joshi AS et al. (2018) Nat Commun "Lipid droplet and peroxisome biogenesis occur at the same ER subdomains."

Golden A, Satpute-Krishnan P, Choudhary V, Nebenfuehr B, Joshi AS, Levine TP, Prinz WA

[Nat Commun, 2018]

Nascent lipid droplet (LD) formation occurs in the endoplasmic reticulum (ER) membrane but it is not known how sites of biogenesis are determined. We previously identified ER domains in S. cerevisiae containing the reticulon homology domain (RHD) protein Pex30 that are regions where preperoxisomal vesicles (PPVs) form. Here, we show that Pex30 domains are also sites where most nascent LDs form. Mature LDs usually remain associated with Pex30 subdomains, and the same Pex30 subdomain can simultaneously associate with a LD and a PPV or peroxisome. We find that in higher eukaryotes multiple C2 domain containing transmembrane protein (MCTP2) is similar to Pex30: it contains an RHD and resides in ER domains where most nascent LD biogenesis occurs and that often associate with peroxisomes. Together, these findings indicate that most LDs and PPVs form and remain associated with conserved ER subdomains, and suggest a link between LD and peroxisome biogenesis.

Joshi T et al. (2007) BMC Genomics "Quantitative assessment of relationship between sequence similarity and function similarity."

Joshi T, Xu D

[BMC Genomics, 2007]

ABSTRACT: BACKGROUND: Comparative sequence analysis is considered as the first step towards annotating new proteins in genome annotation. However, sequence comparison may lead to creation and propagation of function assignment errors. Thus, it is important to perform a thorough analysis for the quality of sequence-based function assignment using large-scale data in a systematic way. RESULTS: We present an analysis of the relationship between sequence similarity and function similarity for the proteins in four model organisms, i.e., Arabidopsis thaliana, Saccharomyces cerevisiae, Caenorrhabditis elegans, and Drosophila melanogaster. Using a measure of functional similarity based on the three categories of Gene Ontology (GO) classifications (biological process, molecular function, and cellular component), we quantified the correlation between functional similarity and sequence similarity measured by sequence identity or statistical significance of the alignment and compared such a correlation against randomly chosen protein pairs. CONCLUSION: Various sequence-function relationships were identified from BLAST versus PSI-BLAST, sequence identity versus Expectation Value, GO indices versus semantic similarity approaches, and within genome versus between genome comparisons, for the three GO categories. Our study provides a benchmark to estimate the confidence in assignment of functions purely based on sequence similarity.

PM Joshi et al. (1999) International C. elegans Meeting "pvl-5 is involved in the early development of the vulva in C. elegans"

DM Eisenmann, PM Joshi

[International C. elegans Meeting, 1999]

The C.elegans vulva is formed from the descendants of the P cells. The 12 P cells, born early in embryogenesis, migrate into the ventral midline by the L1 larval stage where they divide to give an anterior Pn.a neuroblast and a posterior Pn.p hypodermal cell. Of the 12 Pn.p cells, six (P3.p - P8.p) form the vulval equivalence group and are called the vulval precursor cells. On induction by the anchor cell, P5.p, P6.p and P7.p adopt induced cell fates and divide to generate the 22 cells that form the vulva. pvl-5 (ga87) was isolated in a screen for genes affecting the development of the vulva (WBG 13.1, p69). In ga87 animals, there is an average of 7.1 Pn.p cells present in the ventral midline as opposed to 12 Pn.p cells in wildtype. Most probably ga87 is a null mutation as the phenotype of ga87/mnDf39 is no worse than ga87 alone. An additional allele of pvl-5 has been isolated in an F1 non-complementation screen and is being characterized. pvl-5 has been mapped to a small region covered by the deficiency mnDf39 on LGII. The cloning of pvl-5 by cosmid rescue is underway. We do not know why there are too few Pn.p cells in ga87 . It could be either due to a loss of P cells or Pn.p cells by cell death, a failure of P cells to migrate into the ventral midline or a Pn.p to Pn.a cell fate transformation. To distinguish between these possibilities I will use unc-4::gfp which is expressed in the neurons derived from the Pn.a cells (David M. Miller III and Charles J. Niemeyer, Development 121, 2877-2886). In the case of a hypodermal (Pn.p) to a neuroblast (Pn.a) cell fate transformation there will be more unc-4::gfp expressing cells in the ventral nerve cord. If there is a loss of P cells or a failure to migrate there might be fewer unc-4::gfp expressing cells in the VNC. If pvl-5 affects the maintenance of Pn.p cells alone there would be no change in the number of cells expressing the marker. I will also study the P and Pn.p cells using jam-1::gfp (gift of Jeff Simske). jam-1 codes for the protein recognized by the MH27 antibody and hence JAM-1::GFP outlines the boundaries of hypodermal cells. The fate of P cells and their lineage will be followed in a pvl-5(ga87); jam-1::gfp strain. Further results from these experiments will be presented.

Joshi KK et al. (2016) EMBO J "Dopamine signaling promotes the xenobiotic stress response and protein homeostasis."

Joshi KK, Matlack TL, Rongo C

[EMBO J, 2016]

Multicellular organisms encounter environmental conditions that adversely affect protein homeostasis (proteostasis), including extreme temperatures, toxins, and pathogens. It is unclear how they use sensory signaling to detect adverse conditions and then activate stress response pathways so as to offset potential damage. Here, we show that dopaminergic mechanosensory neurons in C.elegans release the neurohormone dopamine to promote proteostasis in epithelia. Signaling through the DA receptor DOP-1 activates the expression of xenobiotic stress response genes involved in pathogenic resistance and toxin removal, and these genes are required for the removal of unstable proteins in epithelia. Exposure to a bacterial pathogen (Pseudomonas aeruginosa) results in elevated removal of unstable proteins in epithelia, and this enhancement requires DA signaling. In the absence of DA signaling, nematodes show increased sensitivity to pathogenic bacteria and heat-shock stress. Our results suggest that dopaminergic sensory neurons, in addition to slowing down locomotion upon sensing a potential bacterial feeding source, also signal to frontline epithelia to activate the xenobiotic stress response so as to maintain proteostasis and prepare for possible infection.