Publications

photoinhibition of respiration in bacteria and the cyanophycea vitreoscilla stercoraria.		1972	11946834
physiological studies on vitreoscilla stercoraria.	vitreoscilla stercoraria atcc 15218 was studied to elucidate some of its physiological characteristics. the initial optimal ph for the organism was found to be 7.5 to 7.7. the characteristics of the growth curve of the organism showed that its growth in shake cultures is by increasing trichome number up to approximately 15 hr and by increasing trichome length after 15 hr. nutritional studies indicated that it is auxotrophic for biotin, thiamine, and l-arginine, and it appears to be an obligate a ...	1972	4565526
nutrition of vitreoscilla stercoraria.	the present study has shown that the glutamate or aspartate families, plus the aromatic amino acid family are required for growth of vitreoscilla stercoraria. furthermore, glutamine can substitute for the glutamate family, asparagine and methionine can replace the aspartate family, and tyrosine can substitute for the aromatic family. amino acids which are easily oxidized by this organism, particularly serine and cysteine, stimulated growth. from these data, a defined medium was devised, which co ...	1975	1220862
unusual sulfonolipids are characteristic of the cytophaga-flexibacter group.	capnocytophaga spp. contain a group of unusual sulfonolipids, called capnoids (w. godchaux iii and e. r. leadbetter, j. bacteriol. 144:592-602, 1980). one of these lipids, capnine, is 2-amino-3-hydroxy-15-methylhexadecane-1-sulfonic acid; the others are, apparently, n-acylated versions of capnine. the lipids were found, in amounts ranging from 2.5 to 16 mumol of capnoid sulfur per g of cells (wet weight), in two cytophaga spp. and also in several closely related organisms: several capnocytophaga ...	1983	6298180
expression, purification, crystallization, and preliminary x-ray diffraction analysis of the homodimeric bacterial hemoglobin from vitreoscilla stercoraria.	the recombinant homodimeric hemoglobin from the strictly aerobe gram-negative bacterium vitreoscilla stercoraria has been expressed in escherichia coli, purified to homogeneity, and crystallized by vapor diffusion techniques, using ammonium sulfate as precipitant. the crystals belong to the monoclinic space group p2(1) and diffract to high resolution. the unit cell parameters are alpha = 62.9, b = 42.5, c = 63.2 a, beta = 106.6 degrees; the asymmetric unit contains the homodimeric hemoglobin, wi ...	1997	9037720
unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from vitreoscilla sp.	the first hemoglobin identified in bacteria was isolated from vitreoscilla stercoraria (vthb) as a homodimeric species. the wild-type protein has been reported to display medium oxygen affinity and cooperative ligand-binding properties. moreover, vthb can support aerobic growth in escherichia coli with impaired terminal oxidase function. this ability of vthb to improve the growth properties of e. coli has important applications in fermentation technology, assisting the overexpression of recombin ...	1997	9115439
bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds.	this study was performed with a laboratory-scale fixed-bed bioreactor degrading a mixture of aromatic compounds (solvesso100). the starter culture for the bioreactor was prepared in a fermentor with a wastewater sample of a care painting facility as the inoculum and solvesso100 as the sole carbon source. the bacterial community dynamics in the fermentor and the bioreactor were examined by a conventional isolation procedure and in situ hybridization with fluorescently labeled rrna-targeted oligon ...	1998	9501433
hemoglobin biosynthesis in vitreoscilla stercoraria dw: cloning, expression, and characterization of a new homolog of a bacterial globin gene.	in the strictly aerobic, gram-negative bacterium vitreoscilla strain c1, oxygen-limited growth conditions create a more than 50-fold increase in the expression of a homodimeric heme protein which was recognized as the first bacterial hemoglobin (hb). the recently determined crystal structure of vitreoscilla hb has indicated that the heme pocket of microbial globins differs from that of eukaryotic hbs. in an attempt to understand the diverse functions of hb-like proteins in prokaryotes, we have c ...	1998	9603838
a cooperative oxygen-binding hemoglobin from mycobacterium tuberculosis.	two putative hemoglobin genes, glbn and glbo, were recently discovered in the complete genome sequence of mycobacterium tuberculosis h37rv. here, we show that the glbn gene encodes a dimeric hemoglobin (hbn) that binds oxygen cooperatively with very high affinity (p(50) = 0.013 mmhg at 20 degrees c) because of a fast combination (25 microm(-1).s(-1)) and a slow dissociation (0.2 s(-1)) rate. resonance raman spectroscopy and ligand association/dissociation kinetic measurements, along with mutagen ...	1999	10500158
expression of alcaligenes eutrophus flavohemoprotein and engineered vitreoscilla hemoglobin-reductase fusion protein for improved hypoxic growth of escherichia coli.	expression of the vhb gene encoding hemoglobin from vitreoscilla sp. (vhb) in several organisms has been shown to improve microaerobic cell growth and enhance oxygen-dependent product formation. the amino-terminal hemoglobin domain of the flavohemoprotein (fhp) of the gram-negative hydrogen-oxidizing bacterium alcaligenes eutrophus has 51% sequence homology with vhb. however, like other flavohemoglobins and unlike vhb, fhp possesses a second (carboxy-terminal) domain with nad(p)h and flavin aden ...	2000	10618209
oligomerization and ligand binding in a homotetrameric hemoglobin: two high-resolution crystal structures of hemoglobin bart's (gamma(4)), a marker for alpha-thalassemia.	hemoglobin (hb) bart's is present in the red blood cells of millions of people worldwide who suffer from alpha-thalassemia. alpha-thalassemia is a disease in which there is a deletion of one or more of the four alpha-chain genes, and excess gamma and beta chains spontaneously form homotetramers. the gamma(4) homotetrameric protein known as hb bart's is a stable species that exhibits neither a bohr effect nor heme-heme cooperativity. although hb bart's has a higher o(2) affinity than either adult ...	2001	11514664
expression of double vitreoscilla hemoglobin enhances growth and alters ribosome and trna levels in escherichia coli.	in several organisms, expression of a gene encoding dimeric hemoglobin (vhb) from the obligate aerobic bacterium vitreoscilla stercoraria has been shown to increase microaerobic cell growth and enhance oxygen-dependent cell metabolism. in an attempt to further improve these effects of vhb, a gene encoding two vhb genes connected by a short linker of six base pairs was constructed and expressed in escherichia coli(double vhb). escherichia coli cells expressing double vhb reached a cell density 19 ...	2002	12052087
extreme uv-a sensitivity of the filamentous gliding bacterium vitreoscilla stercoraria.	strains of the filamentous gliding bacterium vitreoscilla, lb13 and c1, are shown to be highly sensitive to uv-a (320-400 nm), with an ld50 of less than 20 kj m(-2). vitreoscilla lb13 can be protected from uv-a by including superoxide dismutase and catalase, separately or in combination, during the exposure, indicating an involvement of reactive oxygen species. lb13a, a photo-insensitive strain derived from lb13, is described.	2003	12855170
role of an inducible single-domain hemoglobin in mediating resistance to nitric oxide and nitrosative stress in campylobacter jejuni and campylobacter coli.	campylobacter jejuni expresses two hemoglobins, each of which exhibits a heme pocket and structural signatures in common with vertebrate and plant globins. one of these, designated cgb, is homologous to vgb from vitreoscilla stercoraria and does not possess the reductase domain seen in the flavohemoglobins. a cgb-deficient mutant of c. jejuni was hypersensitive to nitrosating agents (s-nitrosoglutathione [gsno] or sodium nitroprusside) and a nitric oxide-releasing compound (spermine nonoate). th ...	2004	15292134
the nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks.	although protein folding domains are generally conserved for function across distant homologous sequences, one crucial structural feature is not conserved: the wrapping of backbone hydrogen bonds, that is, the extent to which they are intramolecularly desolvated and thereby protected from water attack. extensive data on protein complex interfaces led us to postulate that insufficiently wrapped backbone hydrogen bonds in monomeric domains must be adhesive, and therefore determinants of interactiv ...	2004	14978274
exploring the common dynamics of homologous proteins. application to the globin family.	we present a procedure to explore the global dynamics shared between members of the same protein family. the method allows the comparison of patterns of vibrational motion obtained by gaussian network model analysis. after the identification of collective coordinates that were conserved during evolution, we quantify the common dynamics within a family. representative vectors that describe these dynamics are defined using a singular value decomposition approach. as a test case, the globin heme-bi ...	2005	15749782
three globin lineages belonging to two structural classes in genomes from the three kingdoms of life.	although most globins, including the n-terminal domains within chimeric proteins such as flavohemoglobins and globin-coupled sensors, exhibit a 3/3 helical sandwich structure, many bacterial, plant, and ciliate globins have a 2/2 helical sandwich structure. we carried out a comprehensive survey of globins in the genomes from the three kingdoms of life. bayesian phylogenetic trees based on manually aligned sequences indicate the possibility of past horizontal globin gene transfers from bacteria t ...	2005	16061809
structure of a nonheme globin in environmental stress signaling.	rsbr is a regulator of sigma(b), the rna polymerase sigma factor subunit responsible for transcribing the general stress response genes when environmental stress is imposed on bacillus subtilis. the c-terminal domain of rsbr and its paralogues is a substrate for the kinase function of another sigma(b) regulator, rsbt, but the amino acid sequence of the n-terminal domain of rsbr does not reveal any obvious biochemical function. rsbr, its paralogues, and other regulators of sigma(b), including rsb ...	2005	16301540
identification of candidate periodontal pathogens and beneficial species by quantitative 16s clonal analysis.	most studies of the bacterial etiology of periodontitis have used either culture-based or targeted dna approaches, and so it is likely that pathogens remain undiscovered. the purpose of this study was to use culture-independent, quantitative analysis of biofilms associated with chronic periodontitis and periodontal health to identify pathogens and beneficial species. samples from subjects with periodontitis and controls were analyzed using ribosomal 16s cloning and sequencing. several genera, ma ...	2005	16081935
a phylogenomic profile of globins.	globins occur in all three kingdoms of life: they can be classified into single-domain globins and chimeric globins. the latter comprise the flavohemoglobins with a c-terminal fad-binding domain and the gene-regulating globin coupled sensors, with variable c-terminal domains. the single-domain globins encompass sequences related to chimeric globins and "truncated" hemoglobins with a 2-over-2 instead of the canonical 3-over-3 alpha-helical fold.	2006	16600051
recent developments and future prospects of vitreoscilla hemoglobin application in metabolic engineering.	in hypoxic conditions, bacteria express a kind of hemoglobin, which is proposed to enhance respiration and energy metabolism by promoting oxygen delivery. bacteria hemoglobin from vitreoscilla stercoraria - vitreoscilla hemoglobin (vhb), when expressed in various hosts in oxygen-limited conditions, has been shown to improve growth, protein secretion, metabolite productivity and stress resistance of hosts, thus rendering the protein promising in metabolic engineering, especially in plant metaboli ...	2007	17184955
expression of the bacterial hemoglobin gene from vitreoscilla stercoraria increases rifamycin b production in amycolatopsis mediterranei.	it is well known that the culture for rifamycin b production by amycolatopsis mediterranei requires high levels of dissolved oxygen, particularly in industrial processes. in this study, we report the construction of a vector for the expression of the bacterial hemoglobin gene (vhb) from vitreoscilla stercoraria in a rifamycin b-overproducing strain of a. mediterranei. the effect was evaluated in the presence and absence of barbital. the vhb gene was cloned under the control of the perme promoter ...	2008	19111646
a three-dimensional homology model of lipid-free apolipoprotein a-iv using cross-linking and mass spectrometry.	human apolipoprotein a-iv (apoa-iv) is a 46-kda exchangeable plasma protein with many proposed functions. it is involved in chylomicron assembly and secretion, protection from atherosclerosis through a variety of mechanisms, and inhibition of food intake. there is little structural basis for these proposed functions due to the lack of a solved three-dimensional structure of the protein by x-ray crystallography or nmr. based on previous studies, we hypothesized that lipid-free apoa-iv exists in a ...	2008	18430727
shedding light on the role of vitreoscilla hemoglobin on cellular catabolic regulation by proteomic analysis.	heterologous expression of vitreoscilla hemoglobin (vhb) has been reported to improve cell growth, protein synthesis, metabolite productivity and nitric oxide detoxification. although it has been proposed that such phenomenon is attributed to the enhancement of respiration and energy metabolism by facilitating oxygen delivery, the mechanism of vhb action remains to be elucidated. in the present study, changes of protein expression profile in escherichia coli as a consequence of vhb production wa ...	2008	18345284
the single-domain globin from the pathogenic bacterium campylobacter jejuni: novel d-helix conformation, proximal hydrogen bonding that influences ligand binding, and peroxidase-like redox properties.	the food-borne pathogen campylobacter jejuni possesses a single-domain globin (cgb) whose role in detoxifying nitric oxide has been unequivocally demonstrated through genetic and molecular approaches. the x-ray structure of cyanide-bound cgb has been solved to a resolution of 1.35 a. the overall fold is a classic three-on-three alpha-helical globin fold, similar to that of myoglobin and vgb from vitreoscilla stercoraria. however, the d region (defined according to the standard globin fold nomenc ...	2010	20164176
enhanced polyhydroxybutyrate (phb) production via the coexpressed phacab and vgb genes controlled by arabinose p promoter in escherichia coli.	to develop an approach to enhance polyhydroxybutyrate (phb) production via the coexpressed phacab and vgb genes controlled by arabinose p(bad) promoter in escherichia coli.	2010	19943886
relationship between oral malodor and the global composition of indigenous bacterial populations in saliva.	oral malodor develops mostly from the metabolic activities of indigenous bacterial populations within the oral cavity, but whether healthy or oral malodor-related patterns of the global bacterial composition exist remains unclear. in this study, the bacterial compositions in the saliva of 240 subjects complaining of oral malodor were divided into groups based on terminal-restriction fragment length polymorphism (t-rflp) profiles using hierarchical cluster analysis, and the patterns of the microb ...	2010	20228112
functional cis-expression of phacab genes for poly(3-hydroxybutyrate) production by escherichia coli.	to develop a microbial strain producing poly(3-hydroxybutyrate) [p(3hb)], in the absence of antibiotic supplementation (normally required to stabilize a recombinant plasmid), by constructing a recombinant escherichia coli strain with phacab and vgb integrated into the chromosome.	2011	21306405
the presence and role of bacterial quorum sensing in activated sludge.	activated sludge used for wastewater treatment globally is composed of a high-density microbial community of great biotechnological significance. in this study the presence and purpose of quorum sensing via n-acylated-l-homoserine lactones (ahls) in activated sludge was explored. the presence of n-heptanoyl-l-homoserine lactone in organic extracts of sludge was demonstrated along with activation of a luxr-based ahl monitor strain deployed in sludge, indicating ahl-mediated gene expression is act ...	2012	22583685
a stochastic evolutionary model for protein structure alignment and phylogeny.	we present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. indels arise from a classic links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an ornstein-uhlenbeck process. the model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully acc ...	2012	22723302
aerobic expression of vitreoscilla hemoglobin efficiently reduces overflow metabolism in escherichia coli.	overflow metabolism is a prevalent problem for aerobic cultivations of escherichia coli. although several process and molecular approaches have been applied to prevent overflow metabolism, these approaches often result in reductions in growth rate, biomass yield or accumulation of other byproducts. in this report, we present an alternative approach based on increasing the efficiency of aerobic metabolism by the expression of the vitreoscilla stercoraria hemoglobin (vhb) to avoid overflow metabol ...	2014	24677798
enhanced production of ε-caprolactone by coexpression of bacterial hemoglobin gene in recombinant escherichia coli expressing cyclohexanone monooxygenase gene.	baeyer-villiger (bv) oxidation of cyclohexanone to epsilon-caprolactone in a microbial system expressing cyclohexanone monooxygenase (chmo) can be influenced by not only the efficient regeneration of nadph but also a sufficient supply of oxygen. in this study, the bacterial hemoglobin gene from vitreoscilla stercoraria (vhb) was introduced into the recombinant escherichia coli expressing chmo to investigate the effects of an oxygen-carrying protein on microbial bv oxidation of cyclohexanone. coe ...	2014	25269815
enhanced production of fatty acids and astaxanthin in aurantiochytrium sp. by the expression of vitreoscilla hemoglobin.	dissolved oxygen is a critical factor for heterotrophic cell growth and metabolite production. the aim of this study was to investigate the effects of an oxygen-involved protein on cell growth and fatty acid and astaxanthin production in the biologically important thraustochytrid aurantiochytrium sp. the hemoglobin of the vitreoscilla stercoraria (vhb) gene was fused upstream with a zeocin resistance gene (ble) and driven by the aurantiochytrium tubulin promoter. the expression construct was int ...	2014	25420960
open and lys-his hexacoordinated closed structures of a globin with swapped proximal and distal sites.	globins are haem-binding proteins with a conserved fold made up of α-helices and can possess diverse properties. a putative globin-coupled sensor from methylacidiphilum infernorum, hgbrl, contains an n-terminal globin domain whose open and closed structures reveal an untypical dimeric architecture. helices e and f fuse into an elongated helix, resulting in a novel site-swapped globin fold made up of helices a-e, hence the distal site, from one subunit and helices f-h, the proximal site, from ano ...	2015	26094577
effects of genetic modifications and fermentation conditions on 2,3-butanediol production by alkaliphilic bacillus subtilis.	two recombinants of alkaliphilic bacillus subtilis lock 1086, constructed via different strategies such as cloning the gene encoding bacterial hemoglobin from vitreoscilla stercoraria (vhb) and overexpression of the gene encoding acetoin reductase/2,3-butanediol dehydrogenase (bdha) from b. subtilis lock 1086, did not produce more 2,3-butanediol (2,3-bd) than the parental strain. in batch fermentations, this strain synthesized 9.46 g/l in 24 h and 12.80 g/l 2,3-bd in 46 h from sugar beet molasse ...	2016	26590588
overexpression of vitreoscilla hemoglobin increases waterlogging tolerance in arabidopsis and maize.	vitreoscilla hemoglobin (vhb) is a type of hemoglobin found in the gram-negative aerobic bacterium vitreoscilla that has been shown to contribute to the tolerance of anaerobic stress in multiple plant species. maize (zea mays l.) is susceptible to waterlogging, causing significant yield loss. in this study, we approached this problem with the introduction of an exogenous vhb gene.	2016	26833353
an integrated biochemical system for nitrate assimilation and nitric oxide detoxification in bradyrhizobium japonicum.	rhizobia are recognized to establish n2-fixing symbiotic interactions with legume plants. bradyrhizobium japonicum, the symbiont of soybeans, can denitrify and grow under free-living conditions with nitrate (no3 (-)) or nitrite (no2 (-)) as sole nitrogen source. unlike related bacteria that assimilate no3 (-), genes encoding the assimilatory no3 (-) reductase (nasc) and no2 (-) reductase (nira) in b. japonicum are located at distinct chromosomal loci. the nasc gene is located with genes encoding ...	2016	26564204
aerobic expression of vitreoscilla hemoglobin improves the growth performance of cho-k1 cells.	inefficient carbon metabolism is a relevant issue during the culture of mammalian cells for the production of biopharmaceuticals. therefore, cell engineering strategies to improve the metabolic and growth performance of cell lines are needed. the expression of vitreoscilla stercoraria hemoglobin (vhb) has been shown to significantly reduce overflow metabolism and improve the aerobic growth of bacteria. however, the effects of vhb on mammalian cells have been rarely studied. here, the impact of v ...	2017	27906496