Rutgers Creates Joachim Messing Endowed Chair in Molecular Genetics

The Rutgers University Board of Governors today approved the creation of the Joachim Messing Endowed Chair in Molecular Genetics.

Shared Genetics in Humans and Roundworms Shed Light on Infertility, Rutgers Study Finds

McKim Lab Postdoc featured in GSA blog

GSA's Spotlight features authors who make an impact while still in undergrad.

Dr. Gallavotti earns NSF award for latest research initiative

Dismukes research holds great promise for advancing Sustainable Energy

Search for low-cost platinum alternative leads to new technology

Waksman Funded Projects

A list of currently funded research projects as reported by various funding sources.

Located on Busch Campus of Rutgers, The State University of New Jersey, the Waksman Institute of Microbiology is an interdisciplinary research institute devoted to excellence in basic research. Focus areas include developmental biology, cell biology, biochemistry, structural biology, genetics, and genomics.

To support the educational mission of Rutgers, Waksman faculty members hold appointments in academic departments throughout the university. Our researchers train undergraduate students, graduate students, and post-doctoral fellows, as well as engage high school students in research through an outreach program.

Latest News

Dr. Ruth Steward is a Principal Investigator at the Waksman Institute of Microbiology and a member of the Molecular Biology and Biochemistry Department at Rutgers University, New Jersey. Her research focuses on the role of the new Zfrp8 gene, identified in her lab, in hematopoiesis and oogenesis.

From Rutgers Today Pioneering Rutgers professors Richard H. Ebright and Joachim Messing were elected to the prestigious American Academy of Arts and Sciences today. The American Academy of Arts and Sciences is one of the country’s oldest learned societies and independent policy research centers. It convenes academic, business and government leaders to respond to challenges facing  the nation and world.

Gerard Dismukes, distinguished professor, Department of Chemistry and Chemical Biology, and laboratory director of the Waksman Institute of Microbiology, Rutgers University–New Brunswick, is the principal investigator of a three-year award totaling $1.2 million.

Pal Maliga, distinguished professor in the Waksman Institute of Microbiology and professor of plant biology in the Department of Plant Biology and Pathology, has won the Lawrence Bogorad Awar

By Robin Warshaw

Throughout the first half of the 20th century, tuberculosis was one of the nation's most feared killers.

At one point, the highly infectious disease known as TB killed more than 400 Americans a day. But by the early 1950s, TB deaths had dropped sharply – due in large part to research begun years before by a Rutgers University soil microbiologist named Selman Waksman.

Exceptional opportunities are available for highly motivated candidates with strong publication records, regardless of their specific area of expertise. Preferred backgrounds include: molecular biology, algal biology, photosynthesis metabolism, systems biology of microbial metabolism.

Recent Publications

Krishnan, A, Zhang S, Liu Y, Tadmori KA, Bryant DA, Dismukes GC.  2016.  Consequences of ccmR deletion on respiration, fermentation and H2 metabolism in cyanobacterium Synechococcus sp. PCC 7002. Biotechnol Bioeng. Abstract2016_biotechbioeng_krishnan_ccmr_ko_bit25913.pdf
CcmR, a LysR-type transcriptional regulator, represses the genes encoding components of the high-affinity carbon concentration mechanism in cyanobacteria. Unexpectedly, deletion of the ccmR gene was found to alter the expression of the terminal oxidase and fermentative genes, especially the hydrogenase operon in the cyanobacterium Synechococcus sp. PCC 7002. Consistent with the transcriptomic data, the deletion strain exhibits flux increases (30-50%) in both aerobic O2 respiration and anaerobic H2 evolution. To understand how CcmR influences anaerobic metabolism, the kinetics of autofermentation were investigated following photoautotrophic growth. The autofermentative H2 yield increased by 50% in the CcmR deletion strain compared to the wild-type strain, and increased to 160% (within 20 h) upon continuous removal of H2 from the medium ("milking") to suppress uptake. Consistent with this greater reductant flux to H2 , the mutant excreted less lactate during autofermentation (NAD(P)H consuming pathway). To enhance the rate of NADH production during anaerobic metabolism, the ccmR mutant was engineered to introduce GAPDH overexpression (more NADH production) and LDH deletion (less NADH consumption). The triple mutant (ccmR deletion + GAPDH overexpression + LDH deletion) showed 6-8-fold greater H2 yield than the WT strain, achieving conversion rates of 17 nmol 108 cells-1 h-1 and yield of 0.87 H2 per glucose equivalent (8.9% theoretical maximum). Simultaneous monitoring of the intracellular NAD(P)H concentration and H2 production rate by these mutants reveals an inverse correspondence between these variables indicating hydrogenase-dependent H2 production as a major sink for consuming NAD(P)H in preference to excretion of reduced carbon as lactate during fermentation.
Xue, X, Dong J.  2016.  The MAPK substrate MASS2 regulates stomatal patterning in Arabidopsis.. Mol. Reprod. Dev. . 83(2):93.
Vvedenskaya, IO, Vahedian-Movahed H, Zhang Y, Taylor DM, Ebright RH, Nickels BE.  2016.  Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection.. Proceedings of the National Academy of Sciences of the United States of America. 113:E2899-E2905. Abstract
During transcription initiation, RNA polymerase (RNAP) holoenzyme unwinds ∼13 bp of promoter DNA, forming an RNAP-promoter open complex (RPo) containing a single-stranded transcription bubble, and selects a template-strand nucleotide to serve as the transcription start site (TSS). In RPo, RNAP core enzyme makes sequence-specific protein-DNA interactions with the downstream part of the nontemplate strand of the transcription bubble ("core recognition element," CRE). Here, we investigated whether sequence-specific RNAP-CRE interactions affect TSS selection. To do this, we used two next-generation sequencing-based approaches to compare the TSS profile of WT RNAP to that of an RNAP derivative defective in sequence-specific RNAP-CRE interactions. First, using massively systematic transcript end readout, MASTER, we assessed effects of RNAP-CRE interactions on TSS selection in vitro and in vivo for a library of 4(7) (∼16,000) consensus promoters containing different TSS region sequences, and we observed that the TSS profile of the RNAP derivative defective in RNAP-CRE interactions differed from that of WT RNAP, in a manner that correlated with the presence of consensus CRE sequences in the TSS region. Second, using 5' merodiploid native-elongating-transcript sequencing, 5' mNET-seq, we assessed effects of RNAP-CRE interactions at natural promoters in Escherichia coli, and we identified 39 promoters at which RNAP-CRE interactions determine TSS selection. Our findings establish RNAP-CRE interactions are a functional determinant of TSS selection. We propose that RNAP-CRE interactions modulate the position of the downstream end of the transcription bubble in RPo, and thereby modulate TSS selection, which involves transcription bubble expansion or transcription bubble contraction (scrunching or antiscrunching).
Winkelman, JT, Vvedenskaya IO, Zhang Y, Zhang Y, Bird JG, Taylor DM, Gourse RL, Ebright RH, Nickels BE.  2016.  Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection.. Science (New York, N.Y.). 351(6277):1090-3. Abstract
In bacterial transcription initiation, RNA polymerase (RNAP) selects a transcription start site (TSS) at variable distances downstream of core promoter elements. Using next-generation sequencing and unnatural amino acid-mediated protein-DNA cross-linking, we have determined, for a library of 4(10) promoter sequences, the TSS, the RNAP leading-edge position, and the RNAP trailing-edge position. We find that a promoter element upstream of the TSS, the "discriminator," participates in TSS selection, and that, as the TSS changes, the RNAP leading-edge position changes, but the RNAP trailing-edge position does not change. Changes in the RNAP leading-edge position, but not the RNAP trailing-edge position, are a defining hallmark of the "DNA scrunching" that occurs concurrent with RNA synthesis in initial transcription. We propose that TSS selection involves DNA scrunching prior to RNA synthesis.