Simple sequence proteins in prokaryotic proteomes

Subramanyam, Mekapati Bala; Gnanamani, Muthiah; Ramachandran, Srinivasan

doi:10.1186/1471-2164-7-141

Cited by 8 publications

(5 citation statements)

References 38 publications

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“…This is justified by observations that i) disordered proteins/regions in general are implicated in functions related to complexity, such as signaling and transcription regulation [24] , [25] ; ii) structural disorder correlates with complexity at the level of whole genomes, as underlined by the observation that the frequency of disorder increases with increasing complexity of the organism, with a particularly conspicuous increase in evolution between prokaryotes and eukaryotes [23] ; iii) there is a direct link between complexity and disorder in transcription regulation [42] , and iv) there is a significant difference between free-living bacteria, such as Actinobacteria of very complex responses and obligatory parasites, such as Mycoplasma, which are functionally “simple” because they live in a constant environment and cannot respond to many changes. Thus, we reasoned that functional simplification may also be apparent at the level of the whole genome/proteome in the thermal adaptation of bacteria, as already suggested based on observing the correlation of simple sequences of proteins and genome size [43] . Because simple sequences are related to structural disorder, we correlated the proteome size (number of proteins) with average protein disorder ( Figure 3A ).…”

Section: Resultsmentioning

confidence: 86%

Reduction in Structural Disorder and Functional Complexity in the Thermal Adaptation of Prokaryotes

2010

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Genomic correlates of evolutionary adaptation to very low or very high optimal growth temperature (OGT) values have been the subject of many studies. Whereas these provided a protein-structural rationale of the activity and stability of globular proteins/enzymes, the point has been neglected that adaptation to extreme temperatures could also have resulted from an increased use of intrinsically disordered proteins (IDPs), which are resistant to these conditions in vitro. Contrary to these expectations, we found a conspicuously low level of structural disorder in bacteria of very high (and very low) OGT values. This paucity of disorder does not reflect phylogenetic relatedness, i.e. it is a result of genuine adaptation to extreme conditions. Because intrinsic disorder correlates with important regulatory functions, we asked how these bacteria could exist without IDPs by studying transcription factors, known to harbor a lot of function-related intrinsic disorder. Hyperthermophiles have much less transcription factors, which have reduced disorder compared to their mesophilic counterparts. On the other hand, we found by systematic categorization of proteins with long disordered regions that there are certain functions, such as translation and ribosome biogenesis that depend on structural disorder even in hyperthermophiles. In all, our observations suggest that adaptation to extreme conditions is achieved by a significant functional simplification, apparent at both the level of the genome and individual genes/proteins.

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Section: Resultsmentioning

confidence: 86%

Reduction in Structural Disorder and Functional Complexity in the Thermal Adaptation of Prokaryotes

2010

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“…We show that this leads to a more accurate description of amino acid distributions in proteomes ( table 1 ). Consideration of both sequence diversity and amino acid turnover may also help in studying the relationship of amino acid metabolic cost with protein abundance ( Akashi and Gojobori 2002 ; Swire 2007 ; Raiford et al 2008 , 2012 ), with amino acid substitution rates ( Barton et al 2010 ; Heizer et al 2011 ) and with the sequence properties of specific protein classes ( Alves and Savageau 2005 ; Subramanyam et al 2006 ; Perlstein et al 2007 ; Smith and Chapman 2010 ).…”

Section: Discussionmentioning

confidence: 99%

Amino Acid Metabolism Conflicts with Protein Diversity

Krick

Verstraete

Alonso

et al. 2014

Molecular Biology and Evolution

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The 20 protein-coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. On the other hand, a diverse set of protein sequences is necessary to build functional proteomes. Here, we present a simple model for a cost-diversity trade-off postulating that natural proteomes minimize amino acid metabolic flux while maximizing sequence entropy. The model explains the relative abundances of amino acids across a diverse set of proteomes. We found that the data are remarkably well explained when the cost function accounts for amino acid chemical decay. More than 100 organisms reach comparable solutions to the trade-off by different combinations of proteome cost and sequence diversity. Quantifying the interplay between proteome size and entropy shows that proteomes can get optimally large and diverse.

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“…A previous study describes a group of simple sequence proteins (SSPs) in prokaryote genomes, where repeated amino acids are found (Subramanyam et al 2006). Although amino acids such as glycine, proline, alanine, and leucine (the last two highly represented in Rv2707) were frequently found to be repeated both in SSPs and non-SSPs, these amino acids have as a common feature a low biosynthetic cost.…”

Section: Discussionmentioning

confidence: 99%

Characterizing the Mycobacterium tuberculosis Rv2707 protein and determining its sequences which specifically bind to two human cell lines

et al. 2008

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The Rv2707 gene encoding a putative alanine-and leucine-rich protein was found to be present in all Mycobacterium tuberculosis complex strains (by PCR) and its transcription was shown by RT-PCR in all but M. bovis and M. microti. Antibodies raised against Rv2707 peptides specifically recognized the native protein by Western blot and were able to locate this protein on the M. tuberculosis membrane by immunoelectron microscopy. A549 and U937 cells lines were used in binding assays involving synthetic peptides covering the whole Rv2707 protein. ) presented high specific binding to both A549 and U937 cells. Cross-linking assays revealed that peptide 16084 specifically bound to a 40-kDa and a 50-kDa U937 cell membrane protein. High activity binding peptides (HABPs) 16083 and 16084 were able to inhibit M. tuberculosis invasion of A549 cells. Our results suggest that these sequences could be part of the binding sites used by the bacillus for interacting with target cells, and thus represent good candidates to be tested in a future subunit-based, multiepitope, antituberculosis vaccine.

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Simple sequence proteins in prokaryotic proteomes

Cited by 8 publications

References 38 publications

Reduction in Structural Disorder and Functional Complexity in the Thermal Adaptation of Prokaryotes

Reduction in Structural Disorder and Functional Complexity in the Thermal Adaptation of Prokaryotes

Amino Acid Metabolism Conflicts with Protein Diversity

Characterizing the Mycobacterium tuberculosis Rv2707 protein and determining its sequences which specifically bind to two human cell lines

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