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31.
Background
DNA repair is the general term for the collection of critical mechanisms which repair many forms of DNA damage such as methylation or ionizing radiation. DNA repair has mainly been studied in experimental and clinical situations, and relatively few information-based approaches to new extracting DNA repair knowledge exist. As a first step, automatic detection of DNA repair proteins in genomes via informatics techniques is desirable; however, there are many forms of DNA repair and it is not a straightforward process to identify and classify repair proteins with a single optimal method. We perform a study of the ability of homology and machine learning-based methods to identify and classify DNA repair proteins, as well as scan vertebrate genomes for the presence of novel repair proteins. Combinations of primary sequence polypeptide frequency, secondary structure, and homology information are used as feature information for input to a Support Vector Machine (SVM). 相似文献32.
Stabilization of pet operon plasmids and ethanol production in Escherichia coli strains lacking lactate dehydrogenase and pyruvate formate-lyase activities. 总被引:3,自引:0,他引:3
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In the last decade, a major goal of research in biofuels has been to metabolically engineer microorganisms to ferment multiple sugars from biomass or agricultural wastes to fuel ethanol. Escherichia coli strains genetically engineered to contain the pet operon (Zymomonas mobilis pyruvate decarboxylase and alcohol dehydrogenase B genes) produce high levels of ethanol. Strains carrying the pet operon in plasmid (e.g., E. coli B/pLOI297) or in chromosomal (e.g., E. coli KO11) sites require antibiotics in the media to maintain genetic stability and high ethanol productivity. To overcome this requirement, we used the conditionally lethal E. coli strain FMJ39, which carries mutations for lactate dehydrogenase and pyruvate formate lyase and grows aerobically but is incapable of anaerobic growth unless these mutations are complemented. E. coli FBR1 and FBR2 were created by transforming E. coli FMJ39 with the pet operon plasmids pLOI295 and pLOI297, respectively. Both strains were capable of anaerobic growth and displayed no apparent pet plasmid losses after 60 generations in serially transferred (nine times) anaerobic batch cultures. In contrast, similar aerobic cultures rapidly lost plasmids. In high-cell-density batch fermentations, 3.8% (wt/vol) ethanol (strain FBR1) and 4.4% (wt/vol) ethanol (strain FBR2) were made from 10% glucose. Anaerobic, glucose-limited continuous cultures of strain FBR2 grown for 20 days (51 generations; 23 with tetracycline and then 28 after tetracycline removal) showed no loss of antibiotic resistance. Anaerobic, serially transferred batch cultures and high-density fermentations were inoculated with cells taken at 57 generations from the previous continuous culture. Both cultures continued to produce high levels of ethanol in the absence of tetracycline. The genetic stability conferred by selective pressure for pet-containing cells without requirement for antibiotics suggests potential commercial suitability for E. coli FBR1 and FBR2. 相似文献
33.
The ldh gene encoding the
fructose-1,6-diphosphate-dependent L-(+) lactate dehydrogenase from the
ruminal bacterium Streptococcus bovis was cloned and sequenced. A
genomic library of S. bovis JB1 DNA was constructed in lambda ZAP II
and screened by use of a heterologous probe derived from the cloned
Streptococcus mutans ldh gene. Several clones were isolated that
contained a common 2.9-kb fragment as determined by restriction analysis.
Nucleotide sequence analysis revealed a 987-bp open reading frame with
extensive homology to Streptococcus thermophilus and S. mutans
ldh nucleic acid and amino acid sequences. Expression of the cloned
S. bovis ldh gene in Escherichia coli was confirmed by the
ability to complement the ldh mutation of E. coli FMJ39, by
using an in-gel activity screen and by enzymatic assay. Increased LDH
activity was observed in S. bovis JB1 containing the cloned
ldh genes on a multicopy plasmid.
Received: 15 October 1996 / Accepted: 3 December 1996 相似文献
34.
Si?Chen Huicai?Cheng Kristen?N.?Wyckoff Qiang?HeEmail author 《Journal of industrial microbiology & biotechnology》2016,43(6):771-781
To identify potential linkages between specific bacterial populations and process performance in anaerobic digestion, the dynamics of bacterial community structure was monitored with high-throughput sequencing in triplicate anaerobic digesters treating animal waste. Firmicutes and Bacteroidetes were found as the two most abundant populations, however, with contrasting population dynamics in response to organic overloading. Firmicutes dominated the bacterial community during stable process performance at low organic loading rate, representing over 50 % of the bacterial abundance. In contrast, the onset of organic overloading raised the relative abundance of Bacteroidetes from 20 ± 2.6 to 44 ± 3.1 %. In addition to the significant negative correlation between the relative abundance of Firmicutes and Bacteroidetes, populations of Firmicutes and Bacteroidetes were found to be linked to process parameters including organic loading rate, volatile fatty acids concentration, and methane production. Therefore, the population abundance ratio of Firmicutes to Bacteroidetes (F/B ratio) was suggested as a potential indicator for process performance. The interactions between Firmicutes and Bacteroidetes populations could be exploited to develop strategies for the prevention of performance perturbation in anaerobic digestion processes. 相似文献
35.
The structure of ribonuclease-S at 3.5 A resolution 总被引:11,自引:0,他引:11
H W Wyckoff K D Hardman N M Allewell T Inagami L N Johnson F M Richards 《The Journal of biological chemistry》1967,242(17):3984-3988
36.
Ralph W. G. Wyckoff 《The Journal of general physiology》1938,21(3):367-373
Analytical observations have been made with the air ultracentrifuge on concentrated staphylococcus bacteriophage solutions and on these solutions inactivated by alkali, chymo-trypsin, and heat. All active solutions contain a homogeneous heavy component that sediments with a constant of s
20° = ca. 650 x 10–13 cm. sec.–1 dynes–1, has an apparent density of ca. 1.20, and a molecular weight probably not less than 200 millions. There is also present some very light ultraviolet-absorbing material which is not a carrier of bacteriophage activity. The amount of the heavy component is not strictly proportional to the bacteriophage activity so that if the activity resides in it, as appears to be the case, inactivation may occur without measurable change in molecular size and shape. When the bacteriophage solutions are inactivated by chymo-trypsin, the heavy component is not disrupted but the sedimenting boundaries have always been fairly diffuse. As the activity gradually disappears from alkaline solutions, the heavy component is replaced by unsedimentable material. When a solution is inactivated by heating, a dilute gel is produced which sediments with an exceptionally sharp boundary in a relatively intense centrifugal field, 相似文献
37.
T Watanabe N Wada E E Kim H W Wyckoff J Y Chou 《The Journal of biological chemistry》1991,266(31):21174-21178
Human placental and germ cell alkaline phosphatases (PLAP and GCAP, respectively), are characterized by their differential sensitivities to inhibition by L-leucine, EDTA, and heat. Yet, they differ by only 7 amino acids at positions 15, 67, 68, 84, 241, 254, and 429 within their respective 484 residues. To determine the structural basis and the amino acid(s) involved in these physicochemical differences, we constructed three GCAP mutants by site-directed mutagenesis and six GCAP/PLAP chimeras and then expressed these alkaline phosphatase mutants in COS-1 cells. We report that the differential reactivity of PLAP and GCAP depends critically on a single amino acid at position 429. GCAP with Gly-429 is strongly inhibited by L-leucine, EDTA, and heat, whereas PLAP with Glu-429 is resistant. By substituting Gly-429 of GCAP with a series of amino acids, we demonstrate that the relative sensitivities of these mutants to L-leucine, EDTA, and heat inhibition are, in general, parallel. Mutants in the order of resistance to these treatments are: Glu (most resistant), Asp/Ile/Leu, Gln/Val/Lys, Ser/His, and Arg/Thr/Met/Cys/Phe/Trp/Tyr/Pro/Asn/Ala/Gly (least resistant). However, the Ser-429 and His-429 mutants were more resistant to EDTA and heat inhibition than the wild-type GCAP, but were equally sensitive to L-leucine inhibition. Structural analysis of mammalian alkaline phosphatase modeled on the refined crystal structure of Escherichia coli alkaline phosphatase indicates that the negative charge of Glu-429 of PLAP, which simultaneously stabilizes the protein as a whole and the metal binding specifically, probably acts through interactions with the metal ligand His-320 (His-331 in E. coli alkaline phosphatase). Replacement of codon 429 with Gly in GCAP leads to destabilization and loosening of the metal binding. The data suggest that the natural binding site for L-leucine may be near position 429, with the amino and carboxyl groups of L-leucine interacting with bound phosphate and His-432 (His-412 in E. coli alkaline phosphatase), respectively. 相似文献
38.
39.
Vibrio cholerae, the causative agent of cholera, has an absolute requirement for iron and must obtain this element in the human host as well
as in its varied environmental niches. It has multiple systems for iron acquisition, including the TonB-dependent transport
of heme, the endogenous siderophore vibriobactin and several siderophores that are produced by other microorganisms. There
is also a Feo system for the transport of ferrous iron and an ABC transporter, Fbp, which transports ferric iron. There appears
to be at least one additional high affinity iron transport system that has not yet been identified. In iron replete conditions,
iron acquisition genes are repressed by Fur. Fur also represses the synthesis of a small, regulatory RNA, RyhB, which negatively
regulates genes for iron-containing proteins involved in the tricarboxylic acid cycle and respiration as well as genes for
motility and chemotaxis. The redundancy in iron transport systems has made it more difficult to determine the role of individual
systems in vivo and in vitro, but it may reflect the overall importance of iron in the growth and survival of V. cholerae. 相似文献
40.
JB Parentes-Vieira PV Lopes-Costa CG Pires AR dos Santos JD Pereira-Filho BB da Silva 《International Seminars in Surgical Oncology : ISSO》2007,4(1):22