scholarly journals Proteome Mining of Sortase A Dependent Proteins (SDPs) in Lactic Acid Bacteria and Docking Analysis of SDPs interaction with Sortase A

2020 ◽  
Author(s):  
Nahid Javanshir ◽  
Ehsaneh Moslem Rezvani ◽  
Zakie Mazhary ◽  
Sepideh Razani ◽  
Gholamreza Ahmadian ◽  
...  
Keyword(s):  
Amino Acid ◽  
Binding Energy ◽  
Surface Proteins ◽  
Sortase A ◽  
Docking Analysis ◽  
Bacterial Surface ◽  
Host Interaction ◽  
Tract Disorder ◽  
Abundant Amino Acid

Abstract BackgroundLactic acid bacteria (LAB), which are important probiotics, play a fundamental role in ensuring the health of the gastrointestinal tract, maintaining the microbiome balance, and preventing the gastrointestinal (GI) tract disorder. One of the effective mechanisms in the bacterial-host interaction is related to the action of the enzyme sortase A and Sortase Dependent Proteins (SDPs). Sortase plays an important role in the stabilization and retention of the probiotic in the gut by exposing various SDPs on the bacterial surface proteins which is involved in the attachment of bacteria to the host intestine and retention in the gut.ResultsIn this study, out of 165 LABs reference proteomes, there were 25 SDP-free strains. Among the 140 strains with SDPs, 707 proteins were found with the potential to function as SDPs. In this way, ProtScreen software with the ability to recognize a specific motif and domain in the proteome, which is available at http://nigebprotscreen.com/ was designed. Also a database including 707 SDPs in Lactobacillus, Enterococcus, Lactococcus, Carnobacterium, and Leuconostoc strains was designed which is available in the project section at online ProtScreen software. Our results showed that the most abundant amino acid in X position in the LPXTG motif among 165(LABs) is glutamine (Q). Results of SDPs and sortase A docking using HADDOCK and CABS-dock tools, showed that the highest binding energy is related to the glutamine, where a positive relationship between frequency of amino acids and binding energy was observed. Therefore, our data shows that why glutamine in nature and during evolution, has been selected as the best amino acid for X site in LPXTG motif.ConclusionsThe results of the present research and similar studies could be useful in better understanding the role of sortase A and SDPs in the studies on the mechanisms related to the interactions between bacteria and the host, including longer probiotic persistence in the gut.

scholarly journals Proteome Mining of Sortase A Dependent Proteins (SDPs) in Lactic Acid Bacteria and Docking Analysis of SDPs Interaction with Sortase A

2020 ◽  
Author(s):  
Nahid Javanshir ◽  
Ehsaneh Moslem Rezvani ◽  
Zakie Mazhary ◽  
Sepideh Razani ◽  
Gholamreza Ahmadian ◽  
...  
Keyword(s):  
Amino Acids ◽  
Lactic Acid ◽  
Amino Acid ◽  
Binding Energy ◽  
Lactic Acid Bacteria ◽  
Surface Proteins ◽  
Sortase A ◽  
Bacterial Surface ◽  
Lpxtg Motif ◽  
Host Interaction

Abstract Background: Lactic acid bacteria (LAB), which are important probiotics, play a fundamental role in ensuring the health of the gastrointestinal tract, maintaining the microbiome balance, and preventing the gastrointestinal (GI) tract disorder. One of the effective mechanisms in the bacterial-host interaction is related to the action of the enzyme sortase A and Sortase Dependent Proteins (SDPs). Sortase plays an important role in the stabilization and retention of the probiotic in the gut by exposing various SDPs on the bacterial surface proteins which is involved in the attachment of bacteria to the host intestine and retention in the gut.Methods: The present study aimes to identify and investigate the abundance of sortase A-dependent proteins (SDPs) in lactic acide bacteria, as well as the frequency analysis of X residue in the sortase recognition and cleavage LPXTG motif and its effect on the interaction between sortase and SDPs. For this purpose, genomic and proteomic sequences of 165 LABs including 119 Lactobacilli, 29 Enterococci, 8 Lactococci, 5 Carnobacteria, and 4 Leuconostocs, were extracted from UniProt and Genome NCBI databases,. for this, we designed ProtScreen software with the ability to recognize a specific motif and domain in the proteome, which is available at http://nigebprotscreen.com/. Also interactions between sortase A and LPXTG motif with 18 different amino acids in X position were determined using in silico approach. The structure of the sortase A enzyme and a SDP in Lactobacillus acidophilus was used for docking using HADDOCK and CABS-dock toolsResults: In this study, out of 165 LABs reference proteomes, there were 25 SDP-free strains. Among the 140 strains with SDPs, 707 proteins were found with the potential to function as SDPs. In this way, ProtScreen software with the ability to recognize a specific motif and domain in the proteome, which is available at http://nigebprotscreen.com/ was designed. Also a database including 707 SDPs in Lactobacillus, Enterococcus, Lactococcus, Carnobacterium, and Leuconostoc strains was designed which is available in the project section at online ProtScreen software. Our results showed that the most abundant amino acid in X position in the LPXTG motif among 165(LABs) is glutamine (Q). Results of SDPs and sortase A docking using HADDOCK and CABS-dock tools, showed that the highest binding energy is related to the glutamine, where a positive relationship between frequency of amino acids and binding energy was observed. Therefore, our data shows that why glutamine in nature and during evolution, has been selected as the best amino acid for X site in LPXTG motif.Conclusions: The results of the present research and similar studies could be useful in better understanding the role of sortase A and SDPs in the studies on the mechanisms related to the interactions between bacteria and the host, including longer probiotic persistence in the gut.

Two repetitive, biofilm-forming proteins from Staphylococci: from disorder to extension

2015 ◽  
Vol 43 (5) ◽  
pp. 861-866 ◽  
Author(s):  
Fiona Whelan ◽  
Jennifer R. Potts
Keyword(s):  
Medical Device ◽  
Staphylococcus Epidermidis ◽  
Molecular Mechanisms ◽  
Surface Proteins ◽  
Initial Surface ◽  
Surface Attachment ◽  
Bacterial Surface ◽  
Host Interactions ◽  
And Function

Staphylococcus aureus and Staphylococcus epidermidis are an important cause of medical device-related infections that are difficult to treat with antibiotics. Biofilms, in which bacteria are embedded in a bacterially-produced exopolymeric matrix, form on the surface of the implanted medical device. Our understanding of the molecular mechanisms underlying the initial surface attachment and subsequent intercellular interactions as the biofilm matures is improving. Biofilm accumulation can be mediated by a partially deacetylated form of poly-N-acetylglucosamine (PNAG) but, more recently, the role of bacterial surface proteins is being recognized. Here we describe the structure and function of two S. aureus cell surface proteins, FnBPA and SasG, implicated in host interactions and biofilm accumulation. These multifunctional proteins employ intrinsic disorder for distinct molecular outcomes. In the case of FnBPA, disorder generates adhesive arrays that bind fibronectin (Fn); in the case of SasG, disorder is, counterintuitively, used to maintain a strong extended fold.

scholarly journals Review of Lysine Metabolism with a Focus on Humans

2020 ◽  
Vol 150 (Supplement_1) ◽  
pp. 2548S-2555S
Author(s):  
Dwight E Matthews
Keyword(s):  
Amino Acid ◽  
Intestinal Microflora ◽  
Food Sources ◽  
Deficient Diet ◽  
Indispensable Amino Acid ◽  
15N Urea ◽  
Lysine Catabolism ◽  
Abundant Amino Acid ◽  
Lysine Metabolism

ABSTRACT Lysine cannot be synthesized by most higher organisms and, therefore, is an indispensable amino acid (IAA) that must be consumed in adequate amounts to maintain protein synthesis. Although lysine is an abundant amino acid in body proteins, lysine is limited in abundance in many important food sources (e.g. grains). Older observations assigned importance to lysine because animals fed a lysine-deficient diet did not lose weight as fast as animals placed upon other IAA-deficient diets, leading to the theory that there may be a special pool of lysine or metabolites that could be converted to lysine. The first step in the lysine catabolic pathway is the formation of saccharopine and then 2-aminoadipic acid, processes that are mitochondrial. The catabolism of 2-aminoadipic acid proceeds via decarboxylation to a series of CoA esters ending in acetyl-CoA. In mammals, the liver appears to be the primary site of lysine catabolism. In humans, the metabolic and oxidative response of lysine to diets either restricted in protein or in lysine is consistent with what has been measured for other IAAs with isotopically labeled tracers. Intestinal microflora are known to metabolize urea to ammonia and scavenge nitrogen (N) for the synthesis of amino acids. Studies feeding 15N-ammonium chloride or 15N-urea to animals and to humans, demonstrate the appearance of 15N-lysine in gut microbial lysine and in host lysine. However, the amount of 15N-lysine transferred to the host is difficult to assess directly using current methods. It is important to understand the role of the gut microflora in human lysine metabolism, especially in conditions where dietary lysine intake may be limited, but better methods need to be devised.

scholarly journals Extractable Bacterial Surface Proteins in Probiotic–Host Interaction

2018 ◽  
Vol 9 ◽  
Author(s):  
Fillipe L. R. do Carmo ◽  
Houem Rabah ◽  
Rodrigo D. De Oliveira Carvalho ◽  
Floriane Gaucher ◽  
Barbara F. Cordeiro ◽  
...  
Keyword(s):  
Surface Proteins ◽  
Bacterial Surface ◽  
Host Interaction

Insights into the biochemical and functional characterization of sortase E transpeptidase of Corynebacterium glutamicum

2019 ◽  
Vol 476 (24) ◽  
pp. 3835-3847 ◽  
Author(s):  
Aliyath Susmitha ◽  
Kesavan Madhavan Nampoothiri ◽  
Harsha Bajaj
Keyword(s):  
Protein Engineering ◽  
Cell Attachment ◽  
Functional Characterization ◽  
Protein Structures ◽  
Structural Similarity ◽  
Surface Proteins ◽  
Sortase A ◽  
Peptide Cleavage ◽  
New Findings

Most Gram-positive bacteria contain a membrane-bound transpeptidase known as sortase which covalently incorporates the surface proteins on to the cell wall. The sortase-displayed protein structures are involved in cell attachment, nutrient uptake and aerial hyphae formation. Among the six classes of sortase (A–F), sortase A of S. aureus is the well-characterized housekeeping enzyme considered as an ideal drug target and a valuable biochemical reagent for protein engineering. Similar to SrtA, class E sortase in GC rich bacteria plays a housekeeping role which is not studied extensively. However, C. glutamicum ATCC 13032, an industrially important organism known for amino acid production, carries a single putative sortase (NCgl2838) gene but neither in vitro peptide cleavage activity nor biochemical characterizations have been investigated. Here, we identified that the gene is having a sortase activity and analyzed its structural similarity with Cd-SrtF. The purified enzyme showed a greater affinity toward LAXTG substrate with a calculated KM of 12 ± 1 µM, one of the highest affinities reported for this class of enzyme. Moreover, site-directed mutation studies were carried to ascertain the structure functional relationship of Cg-SrtE and all these are new findings which will enable us to perceive exciting protein engineering applications with this class of enzyme from a non-pathogenic microbe.

Schistosomal Sulfotransferase Interaction with Oxamniquine Involves Hybrid Mechanism of Induced-fit and Conformational Selection

2020 ◽  
Vol 16 (4) ◽  
pp. 451-459 ◽  
Author(s):  
Fortunatus C. Ezebuo ◽  
Ikemefuna C. Uzochukwu
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Binding Energy ◽  
Binding Site ◽  
Conformational Dynamics ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Conformational Selection ◽  
Hybrid Mechanism ◽  
Dynamics Simulations

Background: Sulfotransferase family comprises key enzymes involved in drug metabolism. Oxamniquine is a pro-drug converted into its active form by schistosomal sulfotransferase. The conformational dynamics of side-chain amino acid residues at the binding site of schistosomal sulfotransferase towards activation of oxamniquine has not received attention. Objective: The study investigated the conformational dynamics of binding site residues in free and oxamniquine bound schistosomal sulfotransferase systems and their contribution to the mechanism of oxamniquine activation by schistosomal sulfotransferase using molecular dynamics simulations and binding energy calculations. Methods: Schistosomal sulfotransferase was obtained from Protein Data Bank and both the free and oxamniquine bound forms were subjected to molecular dynamics simulations using GROMACS-4.5.5 after modeling it’s missing amino acid residues with SWISS-MODEL. Amino acid residues at its binding site for oxamniquine was determined and used for Principal Component Analysis and calculations of side-chain dihedrals. In addition, binding energy of the oxamniquine bound system was calculated using g_MMPBSA. Results: The results showed that binding site amino acid residues in free and oxamniquine bound sulfotransferase sampled different conformational space involving several rotameric states. Importantly, Phe45, Ile145 and Leu241 generated newly induced conformations, whereas Phe41 exhibited shift in equilibrium of its conformational distribution. In addition, the result showed binding energy of -130.091 ± 8.800 KJ/mol and Phe45 contributed -9.8576 KJ/mol. Conclusion: The results showed that schistosomal sulfotransferase binds oxamniquine by relying on hybrid mechanism of induced fit and conformational selection models. The findings offer new insight into sulfotransferase engineering and design of new drugs that target sulfotransferase.

An ESR study of the peroxidase reaction catalyzed by human methaemoglobin and methaemoglobin-haptoglobin complex

1991 ◽  
Vol 56 (4) ◽  
pp. 923-932
Author(s):  
Jana Stejskalová ◽  
Pavel Stopka ◽  
Zdeněk Pavlíček
Keyword(s):  
Hydrogen Peroxide ◽  
Ascorbic Acid ◽  
Amino Acid ◽  
Peroxidase Activity ◽  
Amino Acid Analysis ◽  
Superoxide Radical ◽  
Esr Spectra ◽  
The Other ◽  
Delocalized Electron

The ESR spectra of peroxidase systems of methaemoglobin-ascorbic acid-hydrogen peroxide and methaemoglobin-haptoglobin complex-ascorbic acid-hydrogen peroxide have been measured in the acetate buffer of pH 4.5. For the system with methaemoglobin an asymmetrical signal with g ~ 2 has been observed which is interpreted as the perpendicular region of anisotropic spectrum of superoxide radical. On the other hand, for the system with methaemoglobin-haptoglobin complex the observed signal with g ~ 2 is symmetrical and is interpreted as a signal of delocalized electron. After realization of three repeatedly induced peroxidase processes the ESR signal of the perpendicular part of anisotropic spectrum of superoxide radical is distinctly diminished, whereas the signal of delocalized electron remains practically unchanged. An amino acid analysis of methaemoglobin along with results of the ESR measurements make it possible to derive a hypothesis about the role of haptoglobin in increasing of the peroxidase activity of methaemoglobin.

10 THE ROLE OF DIETARY L-SERINE IN THE REGULATION OF INTESTINAL MUCUS BARRIER DURING INFLAMMATION

2020 ◽  
Vol 26 (Supplement_1) ◽  
pp. S42-S42
Author(s):  
Kohei Sugihara ◽  
Nobuhiko Kamada
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gut Microbiota ◽  
Control Diet ◽  
Bacterial Strains ◽  
Germ Free ◽  
Intestinal Mucus ◽  
Gnotobiotic Mice ◽  
Mucus Barrier

Abstract Background Recent accumulating evidence suggests that amino acids have crucial roles in the maintenance of intestinal homeostasis. In inflammatory bowel disease (IBD), amino acid metabolism is changed in both host and the gut microbiota. Among amino acids, L-serine plays a central role in several metabolic processes that are essential for the growth and survival of both mammalian and bacterial cells. However, the role of L-serine in intestinal homeostasis and IBD remains incompletely understood. In this study, we investigated the effect of dietary L-serine on intestinal inflammation in a murine model of colitis. Methods Specific pathogen-free (SPF) mice were fed either a control diet (amino acid-based diet) or an L-serine-deficient diet (SDD). Colitis was induced by the treatment of dextran sodium sulfate (DSS). The gut microbiome was analyzed by 16S rRNA sequencing. We also evaluate the effect of dietary L-serine in germ-free mice and gnotobiotic mice that were colonized by a consortium of non-mucolytic bacterial strains or the consortium plus mucolytic bacterial strains. Results We found that the SDD exacerbated experimental colitis in SPF mice. However, the severity of colitis in SDD-fed mice was comparable to control diet-fed mice in germ-free condition, suggesting that the gut microbiota is required for exacerbation of colitis caused by the restriction of dietary L-serine. The gut microbiome analysis revealed that dietary L-serine restriction fosters the blooms of a mucus-degrading bacterium Akkermansia muciniphila and adherent-invasive Escherichia coli in the inflamed gut. Consistent with the expansion of mucolytic bacteria, SDD-fed mice showed a loss of the intestinal mucus layer. Dysfunction of the mucus barrier resulted in increased intestinal permeability, thereby leading to bacterial translocation to the intestinal mucosa, which subsequently increased the severity of colitis. The increased intestinal permeability and subsequent bacterial translocation were observed in SDD-fed gnotobiotic mice that colonized by mucolytic bacteria. In contrast, dietary L-serine restriction did not alter intestinal barrier integrity in gnotobiotic mice that colonized only by non-mucolytic bacteria. Conclusion Our results suggest that dietary L-serine regulates the integrity of the intestinal mucus barrier during inflammation by limiting the expansion of mucus degrading bacteria.

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