Recent lbnl_bs_bao items

Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: insights for transcription-coupled repair and Cockayne Syndrome

Wed, 15 Jun 2022 00:00:00 +0000

Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: insights for transcription-coupled repair and Cockayne Syndrome

Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy.

Wed, 11 May 2022 00:00:00 +0000

Experimental data offers empowering constraints for structure prediction. These constraints can be used to filter equivalently scored models or more powerfully within optimization functions toward prediction. In CASP12, Small Angle X-ray Scattering (SAXS) and Cross-Linking Mass Spectrometry (CLMS) data, measured on an exemplary set of novel fold targets, were provided to the CASP community of protein structure predictors. As solution-based techniques, SAXS and CLMS can efficiently measure states of the full-length sequence in its native solution conformation and assembly. However, this experimental data did not substantially improve prediction accuracy judged by fits to crystallographic models. One issue, beyond intrinsic limitations of the algorithms, was a disconnect between crystal structures and solution-based measurements. Our analyses show that many targets had substantial percentages of disordered regions (up to 40%) or were multimeric or both. Thus, solution measurements...

Insight into the Mechanism of Phenylacetate Decarboxylase (PhdB), a Toluene‐Producing Glycyl Radical Enzyme

Tue, 7 Apr 2020 00:00:00 +0000

We recently reported the discovery of phenylacetate decarboxylase (PhdB), representing one of only ten glycyl-radical-enzyme reaction types known, and a promising biotechnological tool for first-time biochemical synthesis of toluene from renewable resources. Here, we used experimental and computational data to evaluate the plausibility of three candidate PhdB mechanisms, involving either attack at the phenylacetate methylene carbon or carboxyl group [via H-atom abstraction from COOH or single-electron oxidation of COO^- (Kolbe-type decarboxylation)]. In vitro experimental data included assays with F-labeled phenylacetate, kinetic studies, and tests with site-directed PhdB mutants; computational data involved estimation of reaction energetics using density functional theory (DFT). The DFT results indicated that all three mechanisms are thermodynamically challenging (beyond the range of many known enzymes in terms of endergonicity or activation energy barrier), reflecting...

Stop Codon Reassignment in the Wild

Tue, 5 Dec 2017 00:00:00 +0000

Since the discovery of the genetic code and protein translation mechanisms (1), a limited number of variations of the standard assignment between unique base triplets (codons) and their encoded amino acids and translational stop signals have been found in bacteria and phages (2-3). Given the apparent ubiquity of the canonical genetic code, the design of genomically recoded organisms with non-canonical codes has been suggested as a means to prevent horizontal gene transfer between laboratory and environmental organisms (4). It is also predicted that genomically recoded organisms are immune to infection by viruses, under the assumption that phages and their hosts must share a common genetic code (5). This paradigm is supported by the observation of increased resistance of genomically recoded bacteria to phages with a canonical code (4). Despite these assumptions and accompanying lines of evidence, it remains unclear whether differential and non-canonical codon usage represents an...

Genomic and physiological characterization of the chromate-reducing, aquifer-derived firmicute Pelosinus sp. strain HCF1

Fri, 2 May 2014 00:00:00 +0000

Genomic and physiological characterization of the chromate-reducing, aquifer-derived firmicute Pelosinus sp. strain HCF1

Differential isotopic fractionation during Cr(VI) reduction by an aquifer-derived bacterium under arobic versus denitrifying conditions

Tue, 12 Feb 2013 00:00:00 +0000

Differential isotopic fractionation during Cr(VI) reduction by an aquifer-derived bacterium under arobic versus denitrifying conditions

Generalized schemes for high throughput manipulation of the Desulfovibrio vulgaris Hildenborough genome

Fri, 9 Nov 2012 00:00:00 +0000

Generalized schemes for high throughput manipulation of the Desulfovibrio vulgaris Hildenborough genome

Complete genome sequence of Tolumonas auensis type strain (TA 4T)

Wed, 26 Sep 2012 00:00:00 +0000

Tolumonas auensis (Fischer-Romero et al. 1996) is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Other than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4T is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292-bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.

Engineering of bacterial methyl ketone synthesis for biofuels

Mon, 24 Sep 2012 00:00:00 +0000

Engineering of bacterial methyl ketone synthesis for biofuels

Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans

Mon, 24 Sep 2012 00:00:00 +0000

Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans

Biomimetic Actinide Chelators: An Update on the Preclinical Development of the Orally Active Hydroxypyridonate Decorporation Agents 3,4,3-LI(1,2-HOPO) and 5-LIO(Me-3,2-HOPO)

Mon, 17 Sep 2012 00:00:00 +0000

Biomimetic Actinide Chelators: An Update on the Preclinical Development of the Orally Active Hydroxypyridonate Decorporation Agents 3,4,3-LI(1,2-HOPO) and 5-LIO(Me-3,2-HOPO)

The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome

Thu, 23 Jun 2011 00:00:00 +0000

The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome

Genes involved in long-chain alkene biosynthesis in Micrococcus luteus

Mon, 14 Jun 2010 00:00:00 +0000

Aliphatic hydrocarbons are highly appealing targets for advanced cellulosic biofuels, as they are already predominant components of petroleum-based gasoline and diesel fuels. We have studied alkene biosynthesis in Micrococcus luteus ATCC 4698, a close relative of Sarcina lutea (now Kocuria rhizophila), which four decades ago was reported to biosynthesize iso- and anteiso branched, long-chain alkenes. The underlying biochemistry and genetics of alkene biosynthesis were not elucidated in those studies. We show here that heterologous expression of a three-gene cluster from M. luteus (Mlut_13230-13250) in a fatty-acid overproducing E. coli strain resulted in production of long-chain alkenes, predominantly 27:3 and 29:3 (no. carbon atoms: no. C=C bonds). Heterologous expression of Mlut_13230 (oleA) alone produced no long-chain alkenes but unsaturated aliphatic monoketones, predominantly 27:2, and in vitro studies with the purified Mlut_13230 protein and tetradecanoyl-CoA produced...

Genome sequence of the Fleming strain of Micrococcus luteus, a simple free- living actinobacterium

Mon, 14 Jun 2010 00:00:00 +0000

Genome sequence of the Fleming strain of Micrococcus luteus, a simple free- living actinobacterium