Proteomic analysis of post translational modifications in cyanobacteria

Xiong, Qian; Chen, Zhuo; Ge, Feng

doi:10.1016/j.jprot.2015.07.037

Cited by 21 publications

(15 citation statements)

References 129 publications

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“…the 19:19 class β-hairpin in PhaA Syn6909 ), most probably representing the nucleation sites for the protein folding [64], is a good target for point mutations with the scope of improved enzyme efficiency. Interestingly, the sequence alignment detects 13 additional amino acids at the N-terminal end of S. salina PhaA and PhaC which most probably represent the sites of post-translational modifications [52,53]. Moreover, the presence of extra amino acids can confer translational robustness to the protein sequence, against missense errors.…”

Section: Discussionmentioning

confidence: 99%

“…The N-terminal end is characterized by 13 additional amino acids conserved in Synechocystis PhaC proteins (Figure 3). The amino acids His, Trp and Lys, at positions 9, 10 and 12 respectively, are important target amino acids for post-translational modifications, not well understood in prokaryotes [51][52][53]. A codon usage analysis of PhaC Syn6909 ( Figure S4A, red bars) based on the Synechocystis PCC6803 codontable (black bars) resulted in a mean difference of only 9% in codon preference frequency, revealing high accuracy in codon selection [54].…”

Section: Isolation Of Phaa-b Syn6909 and Phae-c Syn6909 Gene Clustersmentioning

confidence: 99%

“…As for PhaC, the PhaA Syn6909 annotated sequence exhibits 13 additional amino acids at the N-terminal end. Also here, some residues (Pro, Asn, Lys) are probably subjected to post-translational modification events [51][52][53]. Panel B of Figure S4 shows the frequency of preferred codons which differ of ca.…”

Section: Isolation Of Phaa-b Syn6909 and Phae-c Syn6909 Gene Clustersmentioning

confidence: 99%

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Identification of Four Polyhydroxyalkanoate Structural Genes in Synechocystis cf. salina PCC6909: In silico Evidences

Silvestrini

Drosg²,

Fritz³

2016

J Proteomics Bioinform

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Section: Discussionmentioning

confidence: 99%

Section: Isolation Of Phaa-b Syn6909 and Phae-c Syn6909 Gene Clustersmentioning

confidence: 99%

Section: Isolation Of Phaa-b Syn6909 and Phae-c Syn6909 Gene Clustersmentioning

confidence: 99%

See 1 more Smart Citation

Identification of Four Polyhydroxyalkanoate Structural Genes in Synechocystis cf. salina PCC6909: In silico Evidences

Silvestrini

Drosg²,

Fritz³

2016

J Proteomics Bioinform

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“…Associating the photosynthetic process with nutrient metabolization, cyanobacteria are able to balance the electrons in their photosynthesis with their metabolism and thus neutralize the reduction caused by reactive oxygen species as a way of protecting against oxidative stress. Cyanobacteria UV-absorbing pigments also play a protective role [ 123 , 124 ]. The adaptive capacity of this phylum is explained in part by its production of secondary metabolites, which makes them competitive for survival in different environments.…”

Section: Cyanobacteriamentioning

confidence: 99%

Cyanobacterial Polyhydroxyalkanoates: A Sustainable Alternative in Circular Economy

2020

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Conventional petrochemical plastics have become a serious environmental problem. Its unbridled use, especially in non-durable goods, has generated an accumulation of waste that is difficult to measure, threatening aquatic and terrestrial ecosystems. The replacement of these plastics with cleaner alternatives, such as polyhydroxyalkanoates (PHA), can only be achieved by cost reductions in the production of microbial bioplastics, in order to compete with the very low costs of fossil fuel plastics. The biggest costs are carbon sources and nutrients, which can be appeased with the use of photosynthetic organisms, such as cyanobacteria, that have a minimum requirement for nutrients, and also using agro-industrial waste, such as the livestock industry, which in turn benefits from the by-products of PHA biotechnological production, for example pigments and nutrients. Circular economy can help solve the current problems in the search for a sustainable production of bioplastic: reducing production costs, reusing waste, mitigating CO2, promoting bioremediation and making better use of cyanobacteria metabolites in different industries.

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“…Besides improving genome annotations, proteogenomic studies can provide valuable information about the presence of post-translational modifications (PTMs) 1 on the proteome-wide level (36 -38). PTMs are a vital cellular control mechanism, which regulates every protein property such as folding, conformation, activity, and functions (39). Almost all the proteins undergo certain amount of PTMs, and this reversible process occurs in most cell compartments to determine the functions of modified protein (40,41).…”

mentioning

confidence: 99%

GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes

Zhang

Yang

Zeng

et al. 2016

Molecular & Cellular Proteomics

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Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of post-translational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predicted H. pylori proteins, identified 20 novel protein coding genes, and corrected four existing gene models with regard to translation initiation sites. In particular, GAPP revealed a large repertoire of PTMs using the same proteomic data and provided a rich resource that can be used to examine the functions of reversible modifications in this human pathogen. This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome annotation efforts for prokaryotes. GAPP is freely available at https://sourceforge.net/ projects/gappproteogenomic/. Molecular & Cellular

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Proteomic analysis of post translational modifications in cyanobacteria

Cited by 21 publications

References 129 publications

Identification of Four Polyhydroxyalkanoate Structural Genes in Synechocystis cf. salina PCC6909: In silico Evidences

Identification of Four Polyhydroxyalkanoate Structural Genes in Synechocystis cf. salina PCC6909: In silico Evidences

Cyanobacterial Polyhydroxyalkanoates: A Sustainable Alternative in Circular Economy

GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes

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