Induced Fit Is a Special Case of Conformational Selection

May 22nd, 2017 by Pradipta Chakraborty and Enrico Di Cera

TOC Graphic

Biochemistry
DOI: 10.1021/acs.biochem.7b00340

The sialate O-acetylesterase EstA from gut Bacteroidetes species enables sialidase-mediated cross-species foraging of 9-O-acetylated sialoglycans [Microbiology]

May 19th, 2017 by Lloyd S Robinson, Warren G Lewis, Amanda L Lewis

The gut harbors many symbiotic, commensal, and pathogenic microbes that engage in the breakdown and metabolism of host carbohydrates. Sialic acids are prominent outermost carbohydrates on mucins and protect underlying glycan chains from enzymatic degradation. Sialidases produced by some members of the colonic microbiota have been shown to promote the expansion of several potential pathogens (e.g. Clostridium difficile, Salmonella, Escherichia coli) that do not produce sialidases. O-acetyl ester modifications of sialic acids help resist the action of many sialidases and are found at high levels in the mammalian colon. However, some gut bacteria, in turn, produce sialylate-O-acetyl esterases to remove them. Here we investigated O-acetylation as a shield against the release of sialic acids by Bacteroidetes sialidases and the subsequent utilization of host sialic acids by commensal and pathogenic strains of E. coli. In vitro foraging studies demonstrated that sialidase-dependent E. coli outgrowth on mucin is enabled by Bacteroides EstA, which acts on glycosidically-linked sialylate-O-acety-esterase substrates, particularly at neutral pH. Biochemical studies suggest that spontaneous migration of O-acetyl esters on the side chain of sialic acid, which can occur at colonic pH, may serve as a switch controlling EstA-assisted sialic acid liberation. Specifically, EstA does not act on O-acetyl esters in their initial 7-position. But, following migration to the 9-position, glycans with O-acetyl esters become susceptible to the sequential enzyme action of bacterial esterases and sialidases. Thus, EstA specifically unlocks the nutritive potential of 9-O-acetylated mucus sialic acids for foraging by bacteria that otherwise lack the means to access this potential carbon source.
  • Posted in Journal of Biological Chemistry, Publications
  • Comments Off on The sialate O-acetylesterase EstA from gut Bacteroidetes species enables sialidase-mediated cross-species foraging of 9-O-acetylated sialoglycans [Microbiology]

Functional regions of the peroxin Pex19 necessary for peroxisome biogenesis [Membrane Biology]

May 19th, 2017 by Gaurav Agrawal, Helen H. Shang, Zhi-Jie Xia, Suresh Subramani

The peroxins Pex19 and Pex3 play an indispensable role in peroxisomal membrane protein (PMP) biogenesis, peroxisome division and inheritance. Pex19 plays multiple roles in these processes, but how these functions relate to the structural organization of the Pex19 domains is unresolved. To this end, using deletion mutants, we mapped the Pex19 regions required for peroxisome biogenesis in the yeast Pichia pastoris. Surprisingly, import-competent peroxisomes still formed when Pex19 domains previously believed to be required for biogenesis were deleted, although the peroxisome size was larger than that in wild-type cells. Moreover, these mutants exhibited a delay of 14-24 h in peroxisome biogenesis. The shortest functional N-terminal (NTCs) and C-terminal constructs (CTCs) were Pex19 (aa 1-150) and Pex19 (aa 89-300), respectively. Deletions of the N-terminal Pex3-binding site disrupted direct interactions of Pex19 with Pex3, but preserved interactions with a membrane peroxisomal targeting signal (mPTS)-binding PMP, Pex10. In contrast, deletion of the C-terminal mPTS-binding domain of Pex19 disrupted its interaction with Pex10, while leaving the Pex19-Pex3 interactions intact. However, Pex11 and Pex25 retained their interactions with both N- and C-terminal deletion mutants. NTC-CTC co-expression improved growth and reverted the larger-than-normal peroxisome size observed with the single deletions. Pex25 was critical for peroxisome formation with the CTC variants, and its overexpression enhanced their interactions with Pex3 and aided the growth of both NTC and CTC Pex19 variants. In conclusion, physical segregation of the Pex3 and PMP-binding domains of Pex19 has provided novel insights into the modular architecture of Pex19. We define the minimum region of Pex19 required for peroxisome biogenesis and a unique role for Pex25 in this process.

Hidden Antioxidative Functions of Reduced Nicotinamide Adenine Dinucleotide Coexisting with Hemoglobin

May 19th, 2017 by Magohei Yamada and Hiromi Sakai

TOC Graphic

ACS Chemical Biology
DOI: 10.1021/acschembio.7b00174
  • Posted in ACS Chemical Biology, Publications
  • Comments Off on Hidden Antioxidative Functions of Reduced Nicotinamide Adenine Dinucleotide Coexisting with Hemoglobin

Corrigendum: Full antagonism of the estrogen receptor without a prototypical ligand side chain

May 17th, 2017 by Sathish Srinivasan

Nature Chemical Biology 13, 691 (2017). doi:10.1038/nchembio0617-691c

Author: Sathish Srinivasan, Jerome C Nwachukwu, Nelson E Bruno, Venkatasubramanian Dharmarajan, Devrishi Goswami, Irida Kastrati, Scott Novick, Jason Nowak, Valerie Cavett, Hai-Bing Zhou, Nittaya Boonmuen, Yuechao Zhao, Jian Min, Jonna Frasor, Benita S Katzenellenbogen, Patrick R Griffin, John A Katzenellenbogen & Kendall W Nettles

  • Posted in Nat Chem Biol, Publications
  • Comments Off on Corrigendum: Full antagonism of the estrogen receptor without a prototypical ligand side chain

Shaping embryonic development

May 17th, 2017 by Nature Chemical Biology - Issue - nature.com science feeds

Nature Chemical Biology 13, 559 (2017). doi:10.1038/nchembio.2403

The growing intersection between chemical tools and principles and developmental biology is providing new insights into the molecular-level details of developmental processes.

The perception of strigolactones in vascular plants

May 17th, 2017 by Shelley Lumba

Nature Chemical Biology 13, 599 (2017). doi:10.1038/nchembio.2340

Authors: Shelley Lumba, Duncan Holbrook-Smith & Peter McCourt

Illuminating developmental biology through photochemistry

May 17th, 2017 by Lukasz Kowalik

Nature Chemical Biology 13, 587 (2017). doi:10.1038/nchembio.2369

Authors: Lukasz Kowalik & James K Chen

Small-molecule pheromones and hormones controlling nematode development

May 17th, 2017 by Rebecca A Butcher

Nature Chemical Biology 13, 577 (2017). doi:10.1038/nchembio.2356

Author: Rebecca A Butcher

  • Posted in Nat Chem Biol, Publications
  • Comments Off on Small-molecule pheromones and hormones controlling nematode development

Optogenetics: Switching with red and blue

May 17th, 2017 by Fuun Kawano

Nature Chemical Biology 13, 573 (2017). doi:10.1038/nchembio.2387

Authors: Fuun Kawano, Fan Shi & Masayuki Yazawa

Multiple optogenetic technologies are required to control biological activity simultaneously with different colors of light. Optimizing a near-infrared-induced heterodimerization system, which can be combined with blue-light-controlled domains, enables precise spatiotemporal control of target molecules in live mammalian cells.