scholarly journals Functional Prediction and Assignment of Methanobrevibacter ruminantium M1 Operome Using a Combined Bioinformatics Approach

2020 ◽  
Vol 11 ◽  
Author(s):  
M. Bharathi ◽  
N. Senthil Kumar ◽  
P. Chellapandi
Keyword(s):  
Binding Proteins ◽  
Metabolic Enzymes ◽  
Methane Formation ◽  
Growth Physiology ◽  
Methanobrevibacter Ruminantium ◽  
Molecular Machinery ◽  
Cellular Machinery ◽  
Insight Into ◽  
Rumen Methanogen ◽  
Successful Technology

Methanobrevibacter ruminantium M1 (MRU) is a rod-shaped rumen methanogen with the ability to use H2 and CO2, and formate as substrates for methane formation in the ruminants. Enteric methane emitted from this organism can also be influential to the loss of dietary energy in ruminants and humans. To date, there is no successful technology to reduce methane due to a lack of knowledge on its molecular machinery and 73% conserved hypothetical proteins (HPs; operome) whose functions are still not ascertained perceptively. To address this issue, we have predicted and assigned a precise function to HPs and categorize them as metabolic enzymes, binding proteins, and transport proteins using a combined bioinformatics approach. The results of our study show that 257 (34%) HPs have well-defined functions and contributed essential roles in its growth physiology and host adaptation. The genome-neighborhood analysis identified 6 operon-like clusters such as hsp, TRAM, dsr, cbs and cas, which are responsible for protein folding, sudden heat-shock, host defense, and protection against the toxicities in the rumen. The functions predicted from MRU operome comprised of 96 metabolic enzymes with 17 metabolic subsystems, 31 transcriptional regulators, 23 transport, and 11 binding proteins. Functional annotation of its operome is thus more imperative to unravel the molecular and cellular machinery at the systems-level. The functional assignment of its operome would advance strategies to develop new anti-methanogenic targets to mitigate methane production. Hence, our approach provides new insight into the understanding of its growth physiology and lifestyle in the ruminants and also to reduce anthropogenic greenhouse gas emissions worldwide.

scholarly journals The Autophagy Machinery in Human-Parasitic Protists; Diverse Functions for Universally Conserved Proteins

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1258
Author(s):  
Hirokazu Sakamoto ◽  
Kumiko Nakada-Tsukui ◽  
Sébastien Besteiro
Keyword(s):  
Membrane Vesicle ◽  
Model Organisms ◽  
Unicellular Eukaryotes ◽  
Current State ◽  
Important Challenge ◽  
Molecular Machinery ◽  
Cellular Machinery ◽  
Apparent Reduction ◽  
Related Proteins ◽  
Genome Projects

Autophagy is a eukaryotic cellular machinery that is able to degrade large intracellular components, including organelles, and plays a pivotal role in cellular homeostasis. Target materials are enclosed by a double membrane vesicle called autophagosome, whose formation is coordinated by autophagy-related proteins (ATGs). Studies of yeast and Metazoa have identified approximately 40 ATGs. Genome projects for unicellular eukaryotes revealed that some ATGs are conserved in all eukaryotic supergroups but others have arisen or were lost during evolution in some specific lineages. In spite of an apparent reduction in the ATG molecular machinery found in parasitic protists, it has become clear that ATGs play an important role in stage differentiation or organelle maintenance, sometimes with an original function that is unrelated to canonical degradative autophagy. In this review, we aim to briefly summarize the current state of knowledge in parasitic protists, in the light of the latest important findings from more canonical model organisms. Determining the roles of ATGs and the diversity of their functions in various lineages is an important challenge for understanding the evolutionary background of autophagy.

scholarly journals Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut

Open Biology ◽  
2016 ◽  
Vol 6 (7) ◽  
pp. 160142 ◽  
Author(s):  
Glyn R. Hemsworth ◽  
Andrew J. Thompson ◽  
Judith Stepper ◽  
Łukasz F. Sobala ◽  
Travis Coyle ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Bacterial Species ◽  
Three Dimensional ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Molecular Machinery ◽  
Bacteroides Ovatus ◽  
Biochemical Analyses ◽  
Individual Specificity

The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta)genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an α-xylosidase, a β-glucosidase, and two α- l -arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins.

Effects of Mechanical Strain on Structural and Actin-Binding Proteins in Neuroblasts

2009 ◽  
Author(s):  
Szu-Yuan Chou ◽  
Chao-Min Cheng ◽  
Yi-Wen Lin ◽  
Chih-Cheng Chen ◽  
Philip R. LeDuc
Keyword(s):  
Sensory Neurons ◽  
Mechanical Stimulation ◽  
Binding Proteins ◽  
Mechanical Strain ◽  
Actin Binding ◽  
Potential Capacity ◽  
Static Mechanical ◽  
Animal Growth ◽  
Mechanical Stretching ◽  
Insight Into

Mechanical stimulation affects the functioning and outgrowth of neurons and has the potential capacity for regeneration. Mechanoreceptors in sensory neurons act as a conduit to respond to pain and touch while neurites experience mechanical stimulation during the process of animal growth. To understand mechanotransduction in neural outgrowth, we used a custom fabricated device to investigate the effects of static mechanical stretching while examining molecular connections such as advillin and actin. Our results have the potential of providing greater understanding of mechanotransduction in neuroblasts, as well as providing insight into mechanical approaches that might be used in increasing neural outgrowth.

Genes encoding light-harvesting chlorophyll a/b-binding proteins in papaya (Carica papaya L.) and insight into lineage-specific evolution in Brassicaceae

Gene ◽  
2020 ◽  
Vol 748 ◽  
pp. 144685
Author(s):  
Zhi Zou ◽  
Meiying Li ◽  
Ruizong Jia ◽  
Hui Zhao ◽  
Pingping He ◽  
...  
Keyword(s):  
Chlorophyll A ◽  
Binding Proteins ◽  
Carica Papaya ◽  
Light Harvesting ◽  
Genes Encoding ◽  
Insight Into

scholarly journals Salicylic Acid Binding Proteins (SABPs): The Hidden Forefront of Salicylic Acid Signalling

2019 ◽  
Vol 20 (18) ◽  
pp. 4377 ◽  
Author(s):  
Igor Pokotylo ◽  
Volodymyr Kravets ◽  
Eric Ruelland
Keyword(s):  
Salicylic Acid ◽  
Binding Proteins ◽  
Redox Status ◽  
Signal Transduction Pathways ◽  
Main Role ◽  
Induced Responses ◽  
Transcriptional Responses ◽  
Plant Life ◽  
Molecular Machinery ◽  
Cell Redox Status

Salicylic acid (SA) is a phytohormone that plays important roles in many aspects of plant life, notably in plant defenses against pathogens. Key mechanisms of SA signal transduction pathways have now been uncovered. Even though details are still missing, we understand how SA production is regulated and which molecular machinery is implicated in the control of downstream transcriptional responses. The NPR1 pathway has been described to play the main role in SA transduction. However, the mode of SA perception is unclear. NPR1 protein has been shown to bind SA. Nevertheless, NPR1 action requires upstream regulatory events (such as a change in cell redox status). Besides, a number of SA-induced responses are independent from NPR1. This shows that there is more than one way for plants to perceive SA. Indeed, multiple SA-binding proteins of contrasting structures and functions have now been identified. Yet, all of these proteins can be considered as candidate SA receptors and might have a role in multinodal (decentralized) SA input. This phenomenon is unprecedented for other plant hormones and is a point of discussion of this review.

scholarly journals Systematic Affiliation and Genome Analysis of Subtercola vilae DB165T with Particular Emphasis on Cold Adaptation of an Isolate from a High-Altitude Cold Volcano Lake

2019 ◽  
Vol 7 (4) ◽  
pp. 107 ◽  
Author(s):  
Alvaro S. Villalobos ◽  
Jutta Wiese ◽  
Johannes F. Imhoff ◽  
Cristina Dorador ◽  
Alexander Keller ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Cold Shock ◽  
Extreme Environment ◽  
Crystal Formation ◽  
Ice Crystal ◽  
Cold Environments ◽  
Ice Binding ◽  
Shock Proteins ◽  
Harsh Conditions ◽  
Insight Into

Among the Microbacteriaceae the species of Subtercola and Agreia form closely associated clusters. Phylogenetic analysis demonstrated three major phylogenetic branches of these species. One of these branches contains the two psychrophilic species Subtercola frigoramans and Subtercola vilae, together with a larger number of isolates from various cold environments. Genomic evidence supports the separation of Agreia and Subtercola species. In order to gain insight into the ability of S. vilae to adapt to life in this extreme environment, we analyzed the genome with a particular focus on properties related to possible adaptation to a cold environment. General properties of the genome are presented, including carbon and energy metabolism, as well as secondary metabolite production. The repertoire of genes in the genome of S. vilae DB165T linked to adaptations to the harsh conditions found in Llullaillaco Volcano Lake includes several mechanisms to transcribe proteins under low temperatures, such as a high number of tRNAs and cold shock proteins. In addition, S. vilae DB165T is capable of producing a number of proteins to cope with oxidative stress, which is of particular relevance at low temperature environments, in which reactive oxygen species are more abundant. Most important, it obtains capacities to produce cryo-protectants, and to combat against ice crystal formation, it produces ice-binding proteins. Two new ice-binding proteins were identified which are unique to S. vilae DB165T. These results indicate that S. vilae has the capacity to employ different mechanisms to live under the extreme and cold conditions prevalent in Llullaillaco Volcano Lake.

scholarly journals A Gene Knock-Down Approach in Tribolium castaneum to Study Survival and Priming Towards Bacillus thuringiensis var. tenebrionis

2021 ◽  
Author(s):  
Ana Sofia Lindeza ◽  
Kathrin Barth ◽  
Joachim Kurtz ◽  
Caroline Zanchi
Keyword(s):  
Tribolium Castaneum ◽  
Defense Mechanisms ◽  
Expression Patterns ◽  
Oral Route ◽  
Immune Defense ◽  
Immune Memory ◽  
Knock Down ◽  
Molecular Machinery ◽  
Defense Molecules ◽  
Insight Into

Insects possess an array of defense molecules allowing them to fight infections. They can also show a form of immune memory, named priming. However, the involvement of insect immune defense mechanisms in priming is unclear, since invertebrates lack the molecular machinery present in vertebrates to build an immune memory. In the red flour beetle Tribolium castaneum, larvae can be primed via the oral route with Bacillus thurigiensis var. tenebrionids (Btt). This results in changes in the expression of a large number of genes, among which some belong to families of ancient defense genes. In the present work, we tested whether three chosen candidate genes (a Thaumatin, a C-type Lectin and an Osiris-like gene) could be involved in the survival to a Btt exposure, as well as in the priming phenotype. We assessed changes in their expression over time and according to the priming treatment, knocked them down individually by RNA interference (RNAi), and observed how it affected survival upon challenge. The quantification of gene expression patterns in our larvae with RT-qPCR showed that up- and/or down-regulation of the genes, after the priming treatment, was quite volatile and time dependent. Upon knock-down, we did not observe the expected decrease in survival to Btt or the abolishment of the priming phenotype. We conclude that knocking down genes individually is probably insufficient to affect survival and priming in our system. This gives us insight into the complexity of the molecular processes underpinning priming.

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