Key words

Caenorhabditis elegans (C.elegans) , genomics, proteomics, development, developmental drift, antagonistic pleiotropy, aging.

Research Interests

Aging limits the normal lifespan of all animals, and is a major risk factor for most diseases. Several model organisms are currently being used to study the aging process including yeast, fruit flies, nematodes, mice, and humans. Of these, the nematode Caenorhabditis elegans is one of the most attractive and useful organisms for studying aging and lifespan. C. elegans normally has a relatively short life span of two weeks, enabling one to assess the effects of different mutations or treatments on lifespan.Although many genes and genetic pathways have been found that specify lifespan, relatively little is known about the differences between young and old worms at either the cellular or molecular levels. My long-term goal is to explore in detail the molecular basis for aging in the nematode C. elegans , by first characterizing the differences between young and old animals and then determining how these changes cause young lively animals to become old and frail.

My previous research in the nematode Caenorhabditis elegans shows that the elt-3/elt-5/elt-6 GATA transcriptional circuit is a developmental pathway that continues functioning throughout the lifespan of the worm. This pathway, which is one of the first and clearest examples of developmental drift, may be in part responsible for the aging of the worm. A key unanswered question is what causes elt-3/elt-5/elt-6 transcriptional drift during aging? In C. elegans , Wnt/Wingless signaling pathways activate elt-5 and elt-6 expression during development. In C. elegans development, Wnt signaling plays a central role in many different processes, such as cell proliferation, differentiation, cell migration, control of cell polarity, axon outgrowth and control of the stem cell niche. In adults, my preliminary results show that mutation in one of the β-catenins, wrm-1 , extends lifespan of other wise wild type animals by ~50%, which indicated that changes in Wnt signaling could account for most age-related changes in gene expression. In addition, my preliminary results show that Wnt signaling is responsible for the increased expression of elt-5/elt-6 during aging. Therefore, I hypothesize that Wnt signaling - a regulator of the elt-3/elt-5/elt-6 transcriptional circuit during normal development - plays an important role in the age-related regulation of this pathway andpossibly many others.

The group will utilize a combination of genomic, bioinformatics, and traditional genetics and molecular biology methods to address the following questions:

(1) Is changes within Wnt signaling pathway cause drift in the elt-3/elt-5/elt-6 transcriptional circuit in old age?

(2) How many other examples are there of developmental drift as a cause for aging in C. elegans ?

(3) Can the aging process be slowed down or may be even reversed by rebalancing either the Wnt signaling pathways, the elt-3/elt-5/elt-6 transcriptional circuit or other newly founded transcriptional circuits?

The results of this work would provide a sound basis for my continued mechanistic studies of aging in C. elegans . I believe that the results of proposed experiments will serve as a strong foundation for developing therapies that could slow down or may be even reverse onset of age-related changes.

Current and available projects:

1. Investigating genetic mechanism of Wnt signaling in ageing in C. elegans.

 We have demonstrated that activity of mom-2/Wnt and cwn-2/Wnt are detrimental for longevity, whereas activity of lin-44/Wnt and egl-20/Wnt are beneficial for long life (ref). A key question is what are the molecular mechanisms that underlie life span extension in mom-2/Wnt or cwn-2/Wnt mutants and life span decrease in lin-44/Wnt and egl-20/Wnt mutants? To answer this question we employ the RNA-seq technique to analyze gene expression changes in each of the four Wnt ligands mutants and wild type worms at day 2 of adulthood. We determine which GO functional categories are significantly enriched among each set of different Wnt ligand regulated genes, and compare Wnt ligand regulated genes to the set of 1254 age-regulated genes.  A key regulatory molecules identified in this and the following projects would be subjected to experimental validation of their role in ageing by post-developmental over-expressing or down-regulating (RNAi) of these genes followed by lifespan screens. If the time of the project permits, the most successful candidates would be further analysed through molecular phenotyping (metabolomics and transcriptomics).  

2.  Characterization of the functional architecture of the Wnt signaling pathway during ageing.

During development, mom-2/Wnt is required to activate sys-1and wrm-1 betta-catenins to promote proper development of the hypodermis. On the other hand lin-44/Wnt is required to activate bar-1/betta-catenin to induce vulva development. In our preliminary results, we determined that mutations in bar-1/betta-catenin extend life span, whereas mutations in lin-44/Wnt shorten life span. This result suggests that lin-44 acts independently of bar-1/betta-catenin. On the other hand, mom-2/Wnt could now utilize all three betta-catenins to promote ageing. To distinguish between these possibilities, we will use the same strategy as in Project 1 to determine if mom-2/Wnt and bar-1, sys-1, and wrm-1 betta-catenins act together or regulate different cascades of events during ageing using RNA-seq technology.  

3.  A genetic screen for pathways involved in regulation of Wnt signaling activity during ageing (two master student projects).

One of the key questions that remain is how Wnt signaling activity itself is regulated? We have begun to answer this question by performing a targeted genetic screen for genes that are involved in regulation of lin-44/Wnt expression during ageing. A great volume of preliminary data has been obtained in the course of a master student project. We selected potential targets by comparing the previously published network of genetic interactions between lin-44/Wnt (http://thebiogrid.org/; and www.genemania.org/) and known ageing genes (http://genomics.senescence.info/genes/). In addition, we included a list of transcription factors that has been show to bind to the promoter of lin-44/Wnt identified in the course of the C. elegans mode ENCODE project (http://www.modencode.org/). We discovered that during ageing, lin-44/Wnt expression and activity is under control of EGF signaling pathway, a known positive regulator of longevity in C. elegans. In the course of this project we would like to continue our screen for factors affecting lin-44/Wnt expression and activity during ageing, as well as applying the same strategy to investigate an upstream regulators of other Wnt ligands. This project would allow us to establish an initial network of signaling cascades that are involved in age-regulation in C. elegans and provide great training projects for master students in various methods of molecular biology and genetics.

• Lazzerini, M., Smith, R.L., and Budovskaya, Y. Developmental drift as a mechanism for ageing: lessons form nematodes. (2013) Biogerontology. (Accepted for publication).

• Lazzerini, M., and Budovskaya, Y. (2013) A dual role of the Wnt signaling pathway during ageing in Caenorhabditis elegans. Aging Cell July 23. PMID:23879250.  

• Smith, R.L., de Boer, R., Brul, S., Budovskaya, Y., van Spek, H. (2013) Premature and accelerated ageing: HIV or HAART?  Frontiers of Genetics in Ageing 3:328. PMID: 23372574. 

• Kim, S.K., Budovskaya, Y.V., Johnson, T.E. Reconciliation of daf-2 suppression by elt-3 in Caenorhabditic elegans from Tonsaker et. al (2012) and Kim et. al. (2012). Mechanisms of Ageing and Development 134(1-2):64-65. PMID: 23262285.
• Anisimov, V.N., Bartke, A., Barzilai, N., Batin, M.A., Blagosklonny, M.V., Brown-Borg, H., Budovskaya, Y.V., Campisi, J., Friguet, B., Fraifeld, V., Franceschi, C., Gems, D., Gladyshev, V., Gorbunova, V., Gudkov, A.V., Kennedy, B., Konovalenko, M., Kraemer, B., Moskalev, A., Petropoulos, I., Pasyukova, E., Rattan, S., Rogina, B., Seluanov, A., Shaposhnikov, M., Shmookler, Reis, R., Tavernarakis, N., Vijg, J., Yashin, A., Zimniak, P. (2012)  “The Second International Conference “Genetics of Ageing and Longevity”.  geing (Albany, NY).]. PMID: 22661237. 
• Kim, S.K., Budovskaya, Y.V., and Johnson, T.E. Response to Tonsaker et.al. (2012) Mechanisms of Ageing and Development 133(1):54-56. PMID: 22155122.
• Budovskaya, Y.V., Wu, K., Southworth, L.K., Jiang, M., Tedesco, P., Johnson, T.E., and Kim, S.K. (2008) An elt-3/elt-5/elt-6 GATA transcription circuit guides aging in C. elegans. CELL 134:291-303.  f1000 star 5. PMID: 18662544.
• Budovskaya, Y.V., Stephan, J.S., Deminoff, S.J., and Herman, P.K. (2005) An evolutionary proteomics approach identifies substrates of the cAMP-dependent protein kinase.  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (39): 13933-13938. PMID: 16172400.
• Budovskaya, Y.V., Stephan, J.S., Reggiori, F., Klionsky, D.J., and Herman, P.K. (2004) The Ras/cAMP-dependent protein kinase signaling pathway regulates an early step of the autophagy process in Saccharomycescerevisiae. JOURNALOF BIOLOGICAL CHEMISTRY 279 (20): 20663-20671. PMID: 15016820. 
• Budovskaya, Y.V., Hama, H., DeWald, D.B.,and Herman, P.K. (2002) The C terminus of the Vps34p phosphoinositide 3-kinase is necessary and sufficient for the interaction with the Vps15p protein kinase. JOURNAL OF BIOLOGICAL CHEMISTRY 277 (1): 287-294. PMID: 12032176.
• Howard, S.C., Budovskaya,Y.V., Chang, Y.W., and Herman, P,K. (2002) The C-terminal domain of the largest subunit of RNA polymerase II is required for stationary phase entry and functionally interacts with the RaS/PKA signaling pathway. JOURNAL OF BIOLOGICAL CHEMISTRY 277 (22): 19488-19497. PMID: 11689570.
• Howard, S.C., Chang, Y.W., Budovskaya, Y.V., and Herman, P,K. (2001) The Ras/PKA signaling pathway of Saccharomyces cerevisiae exhibits a functional interaction with the Sin4p complex of the RNA polymerase II holoenzyme. GENETICS 159 (1): 77-89. PMID: 11560888.
• Chang, Y.W., Howard, S.C., Budovskaya, Y.V., Rine, J., and Herman, P.K. (2001) The rye mutants identify a role for Ssn/Srb proteins of the RNA polymerase II holoenzyme during stationary phase entry in Saccharomyces cerevisiae. GENETICS 157 (1): 17-26. PMID: 11139488.
• Bocharov, E.V., Gudkov, A.T., Budovskaya, E.V., and Arseniev, A.S. (1998) Conformational independence of N- and C-domains in ribosomal protein L7/L12 and in the complex with protein L10. FEBS LETTERS 423 (3): 347-350. PMID: 9515737.
• Gudkov, At., Budovskaya, E.V., and Sherstobaeva, N.M. (1995) The first 37 residues are sufficient for dimerization of ribosomal L7/L12 protein. FEBS LETTERS 367 (3): 280-282. PMID: 7607323.

Protocols:

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Marco Lazzerini (PhD student)

Belinda Koenders-van Sintanneland (Research Assistant)

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