Diversity and function of microbial lipases within the mammalian gut

AbstractBackgroundCurrent estimates suggest the majority of microbial proteins within the mammalian gut lack meaningful annotation. One such functional group are microbial lipases (EC:3.1.1.3), which can alter host access and utilisation of dietary fat. In this paper, we describe the diversity of lipolytic bacteria, including in vitro characterisation of a new lipase.ResultsMetagenomic sequence-based network analysis identified that the majority of microbial lipases in the gut of three host species (human, mouse, pig) belong to two unique clusters. These clusters were characterized by the presence of two novel motifs, AHSKGG and TTxxTPH, which may play a key functional role due to co-localisation in the active site, as identified by structural modelling. Analysis of metagenomic assembled genomes (MAGs) indicated that the majority of lipase-positive species belong to the phylum Firmicutes, although all dominant phyla within the human gut were represented by positive species. Metabolic analysis of these genomes identified a high prevalence of glycerol rather than fatty acid metabolism. The occurrence of microbial lipases determined across ~800 metagenomic gut samples depended on dietary fat consumption, with lipase expression increased in lard fed compared to palm oil fed mice. A representative lipase encoded within the genome of the species Clostridium symbiosum was cloned and its characterization confirmed the in silico prediction and provided detailed annotation to 373 proteins.ConclusionsMicrobial lipases within the gut represent a conserved group characterized by unique amino acid sequence motifs. While an increase in microbial lipase occurrence was positively associated with dietary fat intake, lipase-producing species seemed unable to metabolise the released fatty acids. In this paper, we provide a global analysis of the functional importance and diversity of microbial lipases within the intestine of mammals, which will improve the resolution of future sequence-based studies and open avenues for mechanistic experiments based on isolates.

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Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

eLife ◽

10.7554/elife.68068 ◽

2021 ◽

Vol 10 ◽

Author(s):

Adrian L Sanborn ◽

Benjamin T Yeh ◽

Jordan T Feigerle ◽

Cynthia V Hao ◽

Raphael J L Townshend ◽

...

Keyword(s):

Transcriptional Activation ◽

Structural Constraints ◽

Sequence Motifs ◽

Activation Domains ◽

Activator Proteins ◽

Transcriptional Activation Domain ◽

Shape Complementarity ◽

And Function

Gene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity ('fuzzy' binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology.

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Influence of Operator Site Geometry on Transcriptional Control by the YefM-YoeB Toxin-Antitoxin Complex

Journal of Bacteriology ◽

10.1128/jb.01331-08 ◽

2008 ◽

Vol 191 (3) ◽

pp. 762-772 ◽

Cited By ~ 27

Author(s):

Simon E. S. Bailey ◽

Finbarr Hayes

Keyword(s):

Transcriptional Control ◽

Binding Motif ◽

Sequence Motifs ◽

Conserved Sequence ◽

Short Repeat ◽

Arginine Residues ◽

And Function ◽

Operator Site

ABSTRACT YefM-YoeB is among the most prevalent and well-characterized toxin-antitoxin complexes. YoeB toxin is an endoribonuclease whose activity is inhibited by YefM antitoxin. The regions 5′ of yefM-yoeB in diverse bacteria possess conserved sequence motifs that mediate transcriptional autorepression. The yefM-yoeB operator site arrangement is exemplified in Escherichia coli: a pair of palindromes with core hexamer motifs and a center-to-center distance of 12 bp overlap the yefM-yoeB promoter. YefM is an autorepressor that initially recognizes a long palindrome containing the core hexamer, followed by binding to a short repeat. YoeB corepressor greatly enhances the YefM-operator interaction. Scanning mutagenesis demonstrated that the short repeat is crucial for correct interaction of YefM-YoeB with the operator site in vivo and in vitro. Moreover, altering the relative positions of the two palindromes on the DNA helix abrogated YefM-YoeB cooperative interactions with the repeats: complex binding to the long repeat was maintained but was perturbed to the short repeat. Although YefM lacks a canonical DNA binding motif, dual conserved arginine residues embedded in a basic patch of the protein are crucial for operator recognition. Deciphering the molecular basis of toxin-antitoxin transcriptional control will provide key insights into toxin-antitoxin activation and function.

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Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

10.1101/2020.12.18.423551 ◽

2020 ◽

Author(s):

Adrian L. Sanborn ◽

Benjamin T. Yeh ◽

Jordan T. Feigerle ◽

Cynthia V. Hao ◽

Raphael J. L. Townshend ◽

...

Keyword(s):

Transcriptional Activation ◽

Structural Constraints ◽

Sequence Motifs ◽

Activation Domains ◽

Activator Proteins ◽

Transcriptional Activation Domain ◽

Shape Complementarity ◽

And Function

SUMMARYGene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity (“fuzzy” binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology.

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Molecular architecture and functions of the neuronal cytoskeleton

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100157541 ◽

1990 ◽

Vol 48 (3) ◽

pp. 2-3

Author(s):

Nobutaka Hirokawa

Keyword(s):

Major Elements ◽

Molecular Structures ◽

Organelle Transport ◽

Molecular Architecture ◽

Neuronal Morphogenesis ◽

Microtubule Associated Proteins ◽

Associated Proteins ◽

And Function ◽

Small Clusters

In this symposium I will present our studies about the molecular architecture and function of the cytomatrix of the nerve cells. The nerve cell is a highly polarized cell composed of highly branched dendrites, cell body, and a single long axon along the direction of the impulse propagation. Each part of the neuron takes characteristic shapes for which the cytoskeleton provides the framework. The neuronal cytoskeletons play important roles on neuronal morphogenesis, organelle transport and the synaptic transmission. In the axon neurofilaments (NF) form dense arrays, while microtubules (MT) are arranged as small clusters among the NFs. On the other hand, MTs are distributed uniformly, whereas NFs tend to run solitarily or form small fascicles in the dendrites Quick freeze deep etch electron microscopy revealed various kinds of strands among MTs, NFs and membranous organelles (MO). These structures form major elements of the cytomatrix in the neuron. To investigate molecular nature and function of these filaments first we studied molecular structures of microtubule associated proteins (MAP1A, MAP1B, MAP2, MAP2C and tau), and microtubules reconstituted from MAPs and tubulin in vitro. These MAPs were all fibrous molecules with different length and formed arm like projections from the microtubule surface.

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Decision letter for "Human monocytic myeloid‐derived suppressor cells impair B‐cell phenotype and function in vitro"

10.1002/eji.201948240/v2/decision1 ◽

2019 ◽

Keyword(s):

B Cell ◽

Suppressor Cells ◽

Cell Phenotype ◽

Myeloid Derived Suppressor Cells ◽

And Function

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Review for "Human monocytic myeloid‐derived suppressor cells impair B‐cell phenotype and function in vitro"

10.1002/eji.201948240/v1/review1 ◽

2019 ◽

Keyword(s):

B Cell ◽

Suppressor Cells ◽

Cell Phenotype ◽

Myeloid Derived Suppressor Cells ◽

And Function

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Role of the 807 C/T Polymorphism of the α2 Gene in Platelet GP Ia Collagen Receptor Expression and Function

Thrombosis and Haemostasis ◽

10.1055/s-0037-1614605 ◽

1999 ◽

Vol 81 (06) ◽

pp. 951-956 ◽

Cited By ~ 59

Author(s):

J. Corral ◽

R. González-Conejero ◽

J. Rivera ◽

F. Ortuño ◽

P. Aparicio ◽

...

Keyword(s):

Venous Thrombosis ◽

Cell Types ◽

Receptor Expression ◽

Case Control Studies ◽

Platelet Surface ◽

Vitro Analysis ◽

And Function ◽

In Vitro Analysis

SummaryThe variability of the platelet GP Ia/IIa density has been associated with the 807 C/T polymorphism (Phe 224) of the GP Ia gene in American Caucasian population. We have investigated the genotype and allelic frequencies of this polymorphism in Spanish Caucasians. The T allele was found in 35% of the 284 blood donors analyzed. We confirmed in 159 healthy subjects a significant association between the 807 C/T polymorphism and the platelet GP Ia density. The T allele correlated with high number of GP Ia molecules on platelet surface. In addition, we observed a similar association of this polymorphism with the expression of this protein in other blood cell types. The platelet responsiveness to collagen was determined by “in vitro” analysis of the platelet activation and aggregation response. We found no significant differences in these functional platelet parameters according to the 807 C/T genotype. Finally, results from 3 case/control studies involving 302 consecutive patients (101 with coronary heart disease, 104 with cerebrovascular disease and 97 with deep venous thrombosis) determined that the 807 C/T polymorphism of the GP Ia gene does not represent a risk factor for arterial or venous thrombosis.

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