Identifying pseudogenes from hypothetical proteins for making synthetic proteins

Shidhi, P R; Nair, Achuthsankar S.; Suravajhala, Prashanth

doi:10.1007/s11693-014-9148-4

Cited by 8 publications

(4 citation statements)

References 10 publications

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“…Can structural biology validate such hypothetical proteins that might fundamentally be involved in regulating function? We have earlier looked at the prospects of hypothetical proteins relating pseudogenes to make novel synthetic molecules (Shidhi et al 2014). This will hold a great promise in identifying them as biomarkers and further making better drug targets.…”

Section: Introductionmentioning

confidence: 99%

On Brucella pathogenesis: looking for the unified challenge in systems and synthetic biology

Chiliveru¹,

Appari

Suravajhala³

2014

Syst Synth Biol

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Brucellosis is a zoonotic infection transmitted to humans from infected animals and is one of the widely spread zoonoses. Recently, six species were recognized within the genus Brucella wherein B. melitensis, B. suis and B. abortus are considered virulent for humans. While these species differ phenotypically by their pattern of metabolic activities, there has been an imperative need to understand pathogenesis of Brucella species. It has been foreseen that creating a human vaccine for Brucellosis would entail decreased dose of antibiotics. However the emerging role of Brucella pathogenesis still centers on isolation of the organism and various diagnostic tests thereby leading to varying strategies of treatment cycle. In view of disease heterogeneity, we focus systems and synthetic biology challenges that might improve our understanding the Brucella pathogenesis.

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Section: Introductionmentioning

confidence: 99%

On Brucella pathogenesis: looking for the unified challenge in systems and synthetic biology

Chiliveru¹,

Appari

Suravajhala³

2014

Syst Synth Biol

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“…These disabled copies of genes are the products of gene duplication or retrotransposition of functional genes [37]. It is generally believed that the majority of the HPs are the products of pseudogenes [38]. This feature is employed to check if the HP is actually a pseudogene by performing tBLASTn, a variant of BLAST which considers proteins as a query and searches against the nucleotide database.…”

Section: Methodsmentioning

confidence: 99%

A model to predict the function of hypothetical proteins through a nine-point classification scoring schema

Ijaq

Malik

Kumar³

et al. 2019

BMC Bioinformatics

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BackgroundHypothetical proteins [HP] are those that are predicted to be expressed in an organism, but no evidence of their existence is known. In the recent past, annotation and curation efforts have helped overcome the challenge in understanding their diverse functions. Techniques to decipher sequence-structure-function relationship, especially in terms of functional modelling of the HPs have been developed by researchers, but using the features as classifiers for HPs has not been attempted. With the rise in number of annotation strategies, next-generation sequencing methods have provided further understanding the functions of HPs.ResultsIn our previous work, we developed a six-point classification scoring schema with annotation pertaining to protein family scores, orthology, protein interaction/association studies, bidirectional best BLAST hits, sorting signals, known databases and visualizers which were used to validate protein interactions. In this study, we introduced three more classifiers to our annotation system, viz. pseudogenes linked to HPs, homology modelling and non-coding RNAs associated to HPs. We discuss the challenges and performance of these classifiers using machine learning heuristics with an improved accuracy from Perceptron (81.08 to 97.67), Naive Bayes (54.05 to 96.67), Decision tree J48 (67.57 to 97.00), and SMO_npolyk (59.46 to 96.67).ConclusionWith the introduction of three new classification features, the performance of the nine-point classification scoring schema has an improved accuracy to functionally annotate the HPs.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2554-y) contains supplementary material, which is available to authorized users.

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“…thiooxidans [ 13 , 14 ], and 47% of protein-coding genes from Leptospirillum ferriphilum are of unknown function [ 15 ], a figure that rises to 63% in the case of Ferrovum myxofaciens [ 16 ]. Although many hypothetical genes may correspond to non-functional entities called pseudogenes [ 17 ], it is also likely that many have functions not yet characterized. As such, they could possess novel biological roles that could allow us to gain a deeper and more comprehensive understanding of the mechanisms involved in adaptation to environmental challenges.…”

Section: Introductionmentioning

confidence: 99%

A novel gene from the acidophilic bacterium Leptospirillum sp. CF-1 and its role in oxidative stress and chromate tolerance

et al. 2022

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Background Acidophilic microorganisms like Leptospirillum sp. CF-1 thrive in environments with extremely low pH and high concentrations of dissolved heavy metals that can induce the generation of reactive oxygen species (ROS). Several hypothetical genes and proteins from Leptospirillum sp. CF-1 are known to be up-regulated under oxidative stress conditions. Results In the present work, the function of hypothetical gene ABH19_09590 from Leptospirillum sp. CF-1 was studied. Heterologous expression of this gene in Escherichia coli led to an increase in the ability to grow under oxidant conditions with 5 mM K2CrO4 or 5 mM H2O2. Similarly, a significant reduction in ROS production in E. coli transformed with a plasmid carrying ABH19_09590 was observed after exposure to these oxidative stress elicitors for 30 min, compared to a strain complemented with the empty vector. A co-transcriptional study using RT-PCR showed that ABH19_09590 is contained in an operon, here named the “och” operon, that also contains ABH19_09585, ABH19_09595 and ABH19_09600 genes. The expression of the och operon was significantly up-regulated in Leptospirillum sp. CF-1 exposed to 5 mM K2CrO4 for 15 and 30 min. Genes of this operon potentially encode a NADH:ubiquinone oxidoreductase, a CXXC motif-containing protein likely involved in thiol/disulfide exchange, a hypothetical protein, and a di-hydroxy-acid dehydratase. A comparative genomic analysis revealed that the och operon is a characteristic genetic determinant of the Leptospirillum genus that is not present in other acidophiles. Conclusions Altogether, these results suggest that the och operon plays a protective role against chromate and hydrogen peroxide and is an important mechanism required to face polyextremophilic conditions in acid environments.

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Identifying pseudogenes from hypothetical proteins for making synthetic proteins

Cited by 8 publications

References 10 publications

On Brucella pathogenesis: looking for the unified challenge in systems and synthetic biology

On Brucella pathogenesis: looking for the unified challenge in systems and synthetic biology

A model to predict the function of hypothetical proteins through a nine-point classification scoring schema

A novel gene from the acidophilic bacterium Leptospirillum sp. CF-1 and its role in oxidative stress and chromate tolerance

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