Publications

2012
Ananyev, GM, Skizim NJ, Dismukes CG.  2012.  Enhancing biological hydrogen production from cyanobacteria by removal of excreted products.. Journal of biotechnology. 162(1):97-104. Abstract
Hydrogen is produced by a [NiFe]-hydrogenase in the cyanobacterium Arthrospira (Spirulina) maxima during autofermentation of photosynthetically accumulated glycogen under dark anaerobic conditions. Herein we show that elimination of H₂ backpressure by continuous H₂ removal ("milking") can significantly increase the yield of H₂ in this strain. We show that "milking" by continuous selective consumption of H₂ using an electrochemical cell produces the maximum increase in H₂ yield (11-fold) and H₂ rate (3.4-fold), which is considerably larger than through "milking" by non-selective dilution of the biomass in media (increases H₂ yield 3.7-fold and rate 3.1-fold). Exhaustive autofermentation under electrochemical milking conditions consumes >98% of glycogen and 27.6% of biomass over 7-8 days and extracts 39% of the energy content in glycogen as H₂. Non-selective dilution stimulates H₂ production by shifting intracellular equilibria competing for NADH from excreted products and terminal electron sinks into H₂ production. Adding a mixture of the carbon fermentative products shifts the equilibria towards reactants, resulting in increased intracellular NADH and an increased H₂ yield (1.4-fold). H₂ production is sustained for a period of time up to 7days, after which the PSII activity of the cells decreases by 80-90%, but can be restored by regeneration under photoautotrophic growth.
Liao, JC, Messing J.  2012.  Energy biotechnology. Current opinion in biotechnology. 23(3):287-9.Website
Calviño, M, Messing J.  2012.  Sweet sorghum as a model system for bioenergy crops.. Current opinion in biotechnology. 23(3):323-9. AbstractWebsite
Bioenergy is the reduction of carbon via photosynthesis. Currently, this energy is harvested as liquid fuel through fermentation. A major concern, however, is input cost, in particular use of excess water and nitrogen, derived from an energy-negative process, the Haber-Bosch method. Furthermore, the shortage of arable land creates competition between uses for food and fuel, resulting in increased living expenses. This review seeks to summarize recent knowledge in genetics, genomics, and gene expression of a rising model species for bioenergy applications, sorghum. Its diploid genome has been sequenced, it has favorable low-input cost traits, and genetic crosses between different cultivars can be used to study allelic variations of genes involved in stem sugar metabolism and incremental biomass.
Kolling, DR, Cox N, Ananyev GM, Pace RJ, Dismukes CG.  2012.  What are the oxidation states of manganese required to catalyze photosynthetic water oxidation? Biophysical journal. 103(2):313-22. Abstract
Photosynthetic O(2) production from water is catalyzed by a cluster of four manganese ions and a tyrosine residue that comprise the redox-active components of the water-oxidizing complex (WOC) of photosystem II (PSII) in all known oxygenic phototrophs. Knowledge of the oxidation states is indispensable for understanding the fundamental principles of catalysis by PSII and the catalytic mechanism of the WOC. Previous spectroscopic studies and redox titrations predicted the net oxidation state of the S(0) state to be (Mn(III))(3)Mn(IV). We have refined a previously developed photoassembly procedure that directly determines the number of oxidizing equivalents needed to assemble the Mn(4)Ca core of WOC during photoassembly, starting from free Mn(II) and the Mn-depleted apo-WOC complex. This experiment entails counting the number of light flashes required to produce the first O(2) molecules during photoassembly. Unlike spectroscopic methods, this process does not require reference to synthetic model complexes. We find the number of photoassembly intermediates required to reach the lowest oxidation state of the WOC, S(0), to be three, indicating a net oxidation state three equivalents above four Mn(II), formally (Mn(III))(3)Mn(II), whereas the O(2) releasing state, S(4), corresponds formally to (Mn(IV))(3)Mn(III). The results from this study have major implications for proposed mechanisms of photosynthetic water oxidation.
Skizim, NJ, Ananyev GM, Krishnan A, Dismukes CG.  2012.  Metabolic pathways for photobiological hydrogen production by nitrogenase- and hydrogenase-containing unicellular cyanobacteria Cyanothece.. The Journal of biological chemistry. 287(4):2777-86. Abstract
Current biotechnological interest in nitrogen-fixing cyanobacteria stems from their robust respiration and capacity to produce hydrogen. Here we quantify both dark- and light-induced H(2) effluxes by Cyanothece sp. Miami BG 043511 and establish their respective origins. Dark, anoxic H(2) production occurs via hydrogenase utilizing reductant from glycolytic catabolism of carbohydrates (autofermentation). Photo-H(2) is shown to occur via nitrogenase and requires illumination of PSI, whereas production of O(2) by co-illumination of PSII is inhibitory to nitrogenase above a threshold pO(2). Carbohydrate also serves as the major source of reductant for the PSI pathway mediated via nonphotochemical reduction of the plastoquinone pool by NADH dehydrogenases type-1 and type-2 (NDH-1 and NDH-2). Redirection of this reductant flux exclusively through the proton-coupled NDH-1 by inhibition of NDH-2 with flavone increases the photo-H(2) production rate by 2-fold (at the expense of the dark-H(2) rate), due to production of additional ATP (via the proton gradient). Comparison of photobiological hydrogen rates, yields, and energy conversion efficiencies reveals opportunities for improvement.
Berdygulova, Z, Esyunina D, Miropolskaya N, Mukhamedyarov D, Kuznedelov K, Nickels BE, Severinov K, Kulbachinskiy A, Minakhin L.  2012.  A novel phage-encoded transcription antiterminator acts by suppressing bacterial RNA polymerase pausing.. Nucleic Acids Research. Abstract
Gp39, a small protein encoded by Thermus thermophilus phage P23-45, specifically binds the host RNA polymerase (RNAP) and inhibits transcription initiation. Here, we demonstrate that gp39 also acts as an antiterminator during transcription through intrinsic terminators. The antitermination activity of gp39 relies on its ability to suppress transcription pausing at poly(U) tracks. Gp39 also accelerates transcription elongation by decreasing RNAP pausing and backtracking but does not significantly affect the rates of catalysis of individual reactions in the RNAP active center. We mapped the RNAP-gp39 interaction site to the β flap, a domain that forms a part of the RNA exit channel and is also a likely target for λ phage antiterminator proteins Q and N, and for bacterial elongation factor NusA. However, in contrast to Q and N, gp39 does not depend on NusA or other auxiliary factors for its activity. To our knowledge, gp39 is the first characterized phage-encoded transcription factor that affects every step of the transcription cycle and suppresses transcription termination through its antipausing activity.
Nguyen, TA, Brescic J, Vinyard DJ, Chandrasekar T, Dismukes CG.  2012.  Identification of an oxygenic reaction center psbADC operon in the cyanobacterium Gloeobacter violaceus PCC 7421.. Molecular biology and evolution. 29(1):35-8. Abstract
Gloeobacter violaceus, the earliest diverging oxyphotobacterium (cyanobacterium) on the 16S ribosomal RNA tree, has five copies of the photosystem II psbA gene encoding the D1 reaction center protein subunit. These copies are widely distributed throughout the 4.6 Mbp genome with only one copy colocalizing with other PSII subunits, in marked contrast to all other psbA genes in all publicly available sequenced genomes. A clustering of two other psb genes around psbA3 (glr2322) is unique to Gloeobacter. We provide experimental proof for the transcription of a psbA3DC operon, encoding three of the five reaction center core subunits (D1, D2, and CP43). This is the first example of a transcribed gene cluster containing the D1/D2 or D1/D2/CP43 subunits of PSII in an oxygenic phototroph (prokaryotic or eukaryotic). Implications for the evolution of oxygenic photosynthesis are discussed.
Gardner, GP, Go Y B, Robinson DM, Smith PF, Hadermann J, Abakumov A, Greenblatt M, Dismukes CG.  2012.  Structural requirements in lithium cobalt oxides for the catalytic oxidation of water.. Angewandte Chemie (International ed. in English). 51(7):1616-9.
Srivastava, A, Degen D, Ebright YW, Ebright RH.  2012.  Frequency, Spectrum, and Nonzero Fitness Costs of Resistance to Myxopyronin in Staphylococcus aureus.. Antimicrobial agents and chemotherapy. 56(12):6250-5. Abstract
The antibiotic myxopyronin (Myx) functions by inhibiting bacterial RNA polymerase (RNAP). The binding site on RNAP for Myx-the RNAP "switch region SW1/SW2 subregion"-is different from the binding site on RNAP for the RNAP inhibitor currently used in broad-spectrum antibacterial therapy, rifampin (Rif). Here, we report the frequency, spectrum, and fitness costs of Myx resistance in Staphylococcus aureus. The resistance rate for Myx is 4 × 10(-8) to 7 × 10(-8) per generation, which is equal within error to the resistance rate for Rif (3 × 10(-8) to 10 × 10(-8) per generation). Substitutions conferring Myx resistance were obtained in the RNAP β subunit [six substitutions: V1080(1275)I, V1080(1275)L, E1084(1279)K, D1101(1296)E, S1127(1322)L, and S1127(1322)P] and the RNAP β' subunit [five substitutions: K334(345)N, T925(917)K, T925(917)R, G1172(1354)C, and G1172(1354)D] (residues numbered as in Staphylococcus aureus RNAP and, in parentheses, as in Escherichia coli RNAP). Sites of substitutions conferring Myx resistance map to the RNAP switch region SW1/SW2 subregion and do not overlap the binding site on RNAP for Rif, and, correspondingly, Myx-resistant mutants exhibit no cross-resistance to Rif. All substitutions conferring Myx resistance exhibit significant fitness costs (4 to 15% per generation). In contrast, at least three substitutions conferring Rif resistance exhibit no fitness costs (≤0% per generation). The observation that all Myx-resistant mutants have significant fitness costs whereas at least three Rif-resistant mutants have no fitness costs, together with the previously established inverse correlation between fitness cost and clinical prevalence, suggests that Myx resistance is likely to have lower clinical prevalence than Rif resistance.
Chakraborty, A, Wang D, Ebright YW, Korlann Y, Kortkhonjia E, Kim T, Chowdhury S, Wigneshweraraj S, Irschik H, Jansen R et al..  2012.  Opening and closing of the bacterial RNA polymerase clamp.. Science (New York, N.Y.). 337(6094):591-5. AbstractWebsite
Using single-molecule fluorescence resonance energy transfer, we have defined bacterial RNA polymerase (RNAP) clamp conformation at each step in transcription initiation and elongation. We find that the clamp predominantly is open in free RNAP and early intermediates in transcription initiation but closes upon formation of a catalytically competent transcription initiation complex and remains closed during initial transcription and transcription elongation. We show that four RNAP inhibitors interfere with clamp opening. We propose that clamp opening allows DNA to be loaded into and unwound in the RNAP active-center cleft, that DNA loading and unwinding trigger clamp closure, and that clamp closure accounts for the high stability of initiation complexes and the high stability and processivity of elongation complexes.
Wu, Y, Wang W, Messing J.  2012.  Balancing of sulfur storage in maize seed. BMC plant biology. 12:77. AbstractWebsite
A balanced composition of amino acids in seed flour is critical because of the demand on essential amino acids for nutrition. However, seed proteins in cereals like maize, the crop with the highest yield, are low in lysine, tryptophan, and methionine. Although supplementation with legumes like soybean can compensate lysine deficiency, both crops are also relatively low in methionine. Therefore, understanding the mechanism of methionine accumulation in the seed could be a basis for breeding cultivars with superior nutritional quality.
Wang, W, Wu Y, Messing J.  2012.  The Mitochondrial Genome of an Aquatic Plant, Spirodela polyrhiza.. PloS one. 7(10):e46747. AbstractWebsite
Spirodela polyrhiza is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral features than the Poales. Its complete sequence of the mitochondrial (mt) genome could provide clues for the understanding of the evolution of mt genomes in plant.
Severinov, K, Nair S.  2012.  The action of microcin C and mechanisms of bacterial resistance to it. Future Microbiol. 7:281-289.
Wang, W, Messing J.  2012.  Analysis of ADP-glucose pyrophosphorylase expression during turion formation induced by abscisic acid in Spirodela polyrhiza (greater duckweed). BMC Plant Biology. 12(5) Abstract
Aquatic plants differ in their development from terrestrial plants in their morphology and physiology, but little is known about the molecular basis of the major phases of their life cycle. Interestingly, in place of seeds of terrestrial plants their dormant phase is represented by turions, which circumvents sexual reproduction. However, like seeds turions provide energy storage for starting the next growing season.
Wang, W, Messing J.  2012.  Analysis of ADP-glucose pyrophosphorylase expression during turion formation induced by abscisic acid in Spirodela polyrhiza (greater duckweed). BMC Plant Biol. 12:5. AbstractWebsite
BACKGROUND: Aquatic plants differ in their development from terrestrial plants in their morphology and physiology, but little is known about the molecular basis of the major phases of their life cycle. Interestingly, in place of seeds of terrestrial plants their dormant phase is represented by turions, which circumvents sexual reproduction. However, like seeds turions provide energy storage for starting the next growing season. RESULTS: To begin a characterization of the transition from the growth to the dormant phase we used abscisic acid (ABA), a plant hormone, to induce controlled turion formation in Spirodela polyrhiza and investigated their differentiation from fronds, representing their growth phase, into turions with respect to morphological, ultra-structural characteristics, and starch content. Turions were rich in anthocyanin pigmentation and had a density that submerged them to the bottom of liquid medium. Transmission electron microscopy (TEM) of turions showed in comparison to fronds shrunken vacuoles, smaller intercellular space, and abundant starch granules surrounded by thylakoid membranes. Turions accumulated more than 60% starch in dry mass after two weeks of ABA treatment. To further understand the mechanism of the developmental switch from fronds to turions, we cloned and sequenced the genes of three large-subunit ADP-glucose pyrophosphorylases (APLs). All three putative protein and exon sequences were conserved, but the corresponding genomic sequences were extremely variable mainly due to the invasion of miniature inverted-repeat transposable elements (MITEs) into introns. A molecular three-dimensional model of the SpAPLs was consistent with their regulatory mechanism in the interaction with the substrate (ATP) and allosteric activator (3-PGA) to permit conformational changes of its structure. Gene expression analysis revealed that each gene was associated with distinct temporal expression during turion formation. APL2 and APL3 were highly expressed in earlier stages of turion development, while APL1 expression was reduced throughout turion development. CONCLUSIONS: These results suggest that the differential expression of APLs could be used to enhance energy flow from photosynthesis to storage of carbon in aquatic plants, making duckweeds a useful alternative biofuel feedstock.
Li, Y, Padgett RW.  2012.  bantam is required for optic lobe development and glial cell proliferation. PLoS One. 7(3) AbstractWebsite
microRNAs (miRNAs) are small, conserved, non-coding RNAs that contribute to the control of many different cellular processes, including cell fate specification and growth control. Drosophila bantam, a conserved miRNA, is involved in several functions, such as stimulating proliferation and inhibiting apoptosis in the wing disc. Here, we reported the detailed expression pattern of bantam in the developing optic lobe, and demonstrated a new, essential role in promoting proliferation of mitotic cells in the optic lobe, including stem cells and differentiated glial cells. Changes in bantam levels autonomously affected glial cell number and distribution, and non-autonomously affected photoreceptor neuron axon projection patterns. Furthermore, we showed that bantam promotes the proliferation of mitotically active glial cells and affects their distribution, largely through down regulation of the T-box transcription factor, optomotor-blind (omb, Flybase, bifid). Expression of omb can rescue the bantam phenotype, and restore the normal glial cell number and proper glial cell positioning in most Drosophila brains. These results suggest that bantam is critical for maintaining the stem cell pools in the outer proliferation center and glial precursor cell regions of the optic lobe, and that its expression in glial cells is crucial for their proliferation and distribution.
Westra, ER, van Erp PB, Wong SP, Kunne T, Staals R, Seegers CL, Bollen S, Jore MM, de Vos WM, Dame RT et al..  2012.  CRISPR immunity relies on the conservative binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol. Cell. 46:595-605.
Djordjevic, M, Djordjevic M, Severinov K.  2012.  CRISPR transcript processing: an unusual mechanism for strong amplification of small RNAs. Biol. Direct. 7:24.
Burrows, EH, Bennette NB, Carrieri D, Dixon JL, Brinker A, Frada M, Bakdassabim S N, Falkowski PG, Dismukes GC.  2012.  Dynamics of Lipid Biosynthesis and Redistribution in the Marine Diatom Phaeodactylum tricornutum under Nitrate Deprivation. Bioenerg. Res. 5:876-885. Abstract
One approach to achieve continuous overproduction of lipids in microalgal “cell factories” relies upon depletion or removal of nutrients that act as competing electron sinks (e.g., nitrate and sulfate). However, this strategy can only be effective for bioenergy applications if lipid is synthesized primarily de novo (from CO2 fixation) rather than from the breakdown and interconversion of essential cellular components. In the marine diatom, Phaeodactylum tricornutum, it was determined, using 13C-bicarbonate, that cell growth in nitrate (NO 3 − )-deprived cultures resulted predominantly in de novo lipid synthesis (60 % over 3 days), and this new lipid consisted primarily of triacylglycerides (TAGs). Nearly complete preservation of 12C occurred in all previously existing TAGs in NO 3 − -deprived cultures and thus, further TAG accumulation would not be expected from inhibition of TAG lipolysis. In contrast, both high turnover and depletion of membrane lipids, phosphatidylcholines (PCs), were observed in NO 3 − -deprived cultures (both the headgroups and fatty acid chains), while less turnover was observed in NO 3 − replete cultures. Liquid chromatography-tandem mass spectrometry mass spectra and 13C labeling patterns of PC headgroups provided insight into lipid synthesis in marine diatoms, including suggestion of an internal pool of glycine betaine that feeds choline synthesis. It was also observed that 16C fatty acid chains incorporated into TAGs and PCs contained an average of 14 13C carbons, indicating substantial incorporation of 13C-bicarbonate into fatty acid chains under both nutrient states.
Glukhov, AS, Krutilina AI, Shlyapnikov MG, Severinov K, Lavysh D, Kochetkov VV, McGrath JW, de Leeuwe C, Shaburova OV, Krylov VN et al..  2012.  Genomic analysis of Pseudomonas putida phage tf with localized single-strand DNA interruptions. PLoS One. 7:e51163.
Berdygulova, Z, Esyunina D, Miropolskaya N, Mukhamedyarov D, Kuznedelov K, Nickels B, Severinov K, Kulbachinskiy A, Minakhin L.  2012.  The gp39 protein of phage P23-45 is a transcription antiterminator that acts by suppressing pausing by Thermus thermophilus RNA polymerase. Nucl. Acids Res. 40:4052-4063.
Vvedenskaya, IO, Sharp JS, Goldman SR, Kanabar PN, Livny J, Dove SL, Nickels BE.  2012.  Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs. Genes Dev. 26(13):1498-1507. Abstract
Prokaryotic and eukaryotic RNA polymerases can use 2- to ~4-nt RNAs, ‘‘nanoRNAs,’’ to prime transcription initiation in vitro. It has been proposed that nanoRNA-mediated priming of transcription can likewise occur under physiological conditions in vivo and influence transcription start site selection and gene expression. However, no direct evidence of such regulation has been presented. Here we demonstrate in Escherichia coli that nanoRNAs prime transcription in a growth phase-dependent manner, resulting in alterations in transcription start site selection and changes in gene expression. We further define a sequence element that determines, in part, whether a promoter will be targeted by nanoRNA-mediated priming. By establishing that a significant fraction of transcription initiation is primed in living cells, our findings contradict the conventional model that all cellular transcription is initiated using nucleoside triphosphates (NTPs) only. In addition, our findings identify nanoRNAs as a previously undocumented class of regulatory small RNAs that function by being directly incorporated into a target transcript.
Li, Y., Dooner HK.  2012.  Helitron Proliferation and Gene-Fragment Capture. Topics in Current Genetics, 24: Plant Transposable Elements- Impact on Genome Structure and Function. :193-227.
Park, EC, Ghose P, Shao Z, Ye Q, Kang L, Xu XZ, Powell-Coffman JA, Rongo C.  2012.  Hypoxia regulates glutamate receptor trafficking through an HIF-independent mechanism.. EMBO Journal. Epub ahead of print AbstractWebsite
Oxygen influences behaviour in many organisms, with low levels (hypoxia) having devastating consequences for neuron survival. How neurons respond physiologically to counter the effects of hypoxia is not fully understood. Here, we show that hypoxia regulates the trafficking of the glutamate receptor GLR-1 in C. elegans neurons. Either hypoxia or mutations in egl-9, a prolyl hydroxylase cellular oxygen sensor, result in the internalization of GLR-1, the reduction of glutamate-activated currents, and the depression of GLR-1-mediated behaviours. Surprisingly, hypoxia-inducible factor (HIF)-1, the canonical substrate of EGL-9, is not required for this effect. Instead, EGL-9 interacts with the Mint orthologue LIN-10, a mediator of GLR-1 membrane recycling, to promote LIN-10 subcellular localization in an oxygen-dependent manner. The observed effects of hypoxia and egl-9 mutations require the activity of the proline-directed CDK-5 kinase and the CDK-5 phosphorylation sites on LIN-10, suggesting that EGL-9 and CDK-5 compete in an oxygen-dependent manner to regulate LIN-10 activity and thus GLR-1 trafficking. Our findings demonstrate a novel mechanism by which neurons sense and respond to hypoxia.
Shadrin, A, Sheppard C, Matthews S, Severinov K, Wigneshweraraj S.  2012.  Inhibition of transcription initiation by T7 Gp2 occurs through at least two different sets of interactions with the E. coli RNA polymerase. Microbiology SGM. 158:2753-2764.